Helios NanoLab 

450 / 450 S / 450 ML / 650 / 600i

User Operation Manual

Edition 2
23 Feb, 2012
 Trademark Acknowledgments

The FEI logo, AutoLoader are trademarks of FEI Company.

FEI is a registered trademark of FEI Company.
Microsoft® and Windows XP™ are registered trademarks of Microsoft Corporation.
This manual was produced using FrameMaker™ document publishing software.
FrameMaker™ and Adobe are registered trademarks of Adobe Systems Incorporated.
Other product and company names mentioned herein may be the trademarks of their respective owners.

Copyright © 2011 by FEI Company

The information and materials contained herein are confidential and proprietary to FEI Company.
They are provided for your organization's internal use on a need-to-know basis.
They cannot be duplicated or disseminated for any third party without the express consent of FEI Company.

Limited Rights

The following notice applies to the U.S. Government and other purchases with federal funds:
Contractor Name:
FEI Company
Contractor Address:
5350 NE Dawson Creek Drive, Hillsboro, OR 97124
The Government's rights to use, modify, reproduce, release, perform, display, or disclose these technical data
are restricted to those rights specified in:
DFARS 252.227-7015(b)(2), FAR 52.227-14(g)(2) (Alternate II) and FAR 12.211.
Any reproduction of technical data or portions thereof marked with this legend
must also reproduce the markings.
Any person, other than the Government, who has been provided access to such data,
must promptly notify the above named Contractor.

Technical Writer

Martin Dufek
TABLE OF CONTENTS

Chapter 1 System Overview

User Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
FEI Microscope Systems Safety Manual . . . . . . . . . . . . . . . . . . . . 1-1
User Operation Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
System Capabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
System Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Computer Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Vacuum System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Stage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Image Viewing and Capture . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Beams Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Gas Injection System (GIS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
Analysis Capability. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5

Chapter 2 System Control

Interface Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Software v5.1.X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Microscope Console Control Panel . . . . . . . . . . . . . . . . . . . . . . . 2-2
Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
Vacuum Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
Pump button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
Vent button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
System States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Power Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8
Emergency Off. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8
Equipments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
Detector Types and Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
PlasmaCleaner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
Stages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
X-section Sample Holder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
Loadlock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Multiloader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Nav-Cam (in-chamber) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Stage movement limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12

Chapter 3 Software Control

Software Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Other Software and Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Software Interface Elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Tool-Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Pull-down Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Using the Mouse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Using the Keyboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Command Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
List Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3

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Property Editors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3

Edit Boxes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
Radio Buttons / Check Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
Adjusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Exponential Adjuster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Linear Adjuster. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Preset Adjuster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Spinner. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
2D Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Dialogues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Progress bars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
xT microscope Server Software . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
xT microscope Control Software . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
Title Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
Menu Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
File Menu (Alt + F) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
Edit Menu (Alt + E). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
Detectors Menu (Alt + D) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
Scan Menu (Alt + C) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-11
Beam Menu (Alt + B) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-14
Patterning Menu (Alt + P) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15
Stage Menu (Alt + S) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-16
Tools Menu (Alt + T) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18
Window Menu (Alt + W) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-20
Help Menu (Alt + H) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-22
Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-23
Magnification / High Voltage / Beam current List Boxes . . . . . . 3-23
Imaging Pixel Resolution List Box . . . . . . . . . . . . . . . . . . . . . . . 3-23
Direct Measurement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-23
FIBI (FIB Immersion) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-23
Imaging Area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-24
Image Databar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-24
Pages (Alt + P) and Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-25
1. Vacuum Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-25
2. System Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-26
3. Column Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-26
4. Magnification Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-26
5. Scan Rotation Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-26
6. Beam Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-27
7. Beam Deceleration Module . . . . . . . . . . . . . . . . . . . . . . . . . . 3-27
8. Detectors Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-27
9. Status Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-28
10. Stage Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-28
11. Stage Z Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-29
12. LoadLock Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-29
13. Pattern Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-30
14. Omniprobe Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-30
15. End Point Monitor Module . . . . . . . . . . . . . . . . . . . . . . . . . . 3-31
16. Measurement / Annotation Module . . . . . . . . . . . . . . . . . . . 3-31
17. Digital Zoom Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-31
18. Enhanced Image Module . . . . . . . . . . . . . . . . . . . . . . . . . . 3-32
19. Detector settings Module . . . . . . . . . . . . . . . . . . . . . . . . . . 3-32
20. Quad Presets Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-33
21. Alignments Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-33
FEI User Management Software . . . . . . . . . . . . . . . . . . . . . . . . . . 3-34
Control possibilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-34

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FEI Account Administrators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-34

File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-35
Account Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-35
Userdata menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-36
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-36
Account Logging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-36
Preferences… Dialogue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-37
Units Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-37
Movie Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-38
Databar Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-38
Presets Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-39
Scanning Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-40
Sensitivity Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-41
General Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-42
Magnification Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-45
Entering Commands in Summary . . . . . . . . . . . . . . . . . . . . . . . . 3-46
Using Mouse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-46
Using Keyboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-47

Chapter 4 Alignments
Common Rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Buttons and Control Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Alignment list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
5 - Emitter Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
17 - Quick Stage Rotation Center Alignment . . . . . . . . . . . . . . . . 4-5
18 - Accurate Stage Rotation Center Alignment . . . . . . . . . . . . . . 4-7
65 - UHR-FIB wait time configuration . . . . . . . . . . . . . . . . . . . . . . 4-8
100 - Vacuum: Start IGP’s . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9
102 - Vacuum: User Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10
104 - Plasma Cleaning Alignment . . . . . . . . . . . . . . . . . . . . . . . . 4-11
105 - Pre-vacuum Pump Operation . . . . . . . . . . . . . . . . . . . . . . . 4-12
114 - Gas Flush Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-13
210 - ION: Beam Alignment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-14
211 - FIB-I Ion Column Alignment . . . . . . . . . . . . . . . . . . . . . . . . 4-15
253 - Supervisor: Ion Beam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-17
254 - Supervisor: GIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-18
E-Column: / Vacuum Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-19
Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-20
E-Column: UC User Alignments . . . . . . . . . . . . . . . . . . . . . . . . . . 4-21
E-Column: User Alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-22
E-Column: Aperture Map Selection . . . . . . . . . . . . . . . . . . . . . . . 4-23
E-Column: Magnification Correction . . . . . . . . . . . . . . . . . . . . . . 4-24
E-column: Auto UMode Source Centering . . . . . . . . . . . . . . . . . 4-25
E-Column: UC Supervisor Alignments . . . . . . . . . . . . . . . . . . . . 4-26
E-Column: Supervisor Alignments . . . . . . . . . . . . . . . . . . . . . . . 4-27
E-column: U-mode Aperture Selection . . . . . . . . . . . . . . . . . . . . 4-28
Vacuum Actions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-29

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Chapter 5 Operating Procedures

Specimen Preparation and Handling . . . . . . . . . . . . . . . . . . . . . . . 5-2
Needed items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Coated Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Mounting Specimen on Holder . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Microscope Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
Operation Pre-Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
Obtaining ImagING on Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4
Imaging Optimising . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
Principles of SEM imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
Magnification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
Changing Magnification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Scan Speed and Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Contrast and Brightness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Using Videoscope (F3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Focusing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Focusing with MUI (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Correcting Astigmatism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Direct Adjustments (Ctrl + F8) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Ion Beam tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Ion Stigmator Centering tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Electron Beam tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Electron Stigmator Centering tab. . . . . . . . . . . . . . . . . . . . . . . . 5-10
Digital Imaging Enhancement / Imaging Mixing / Coloring . . . . . . 5-11
Standard Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13
Everhart Thornley Detector (ETD) . . . . . . . . . . . . . . . . . . . . . . . . 5-13
ETD Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13
Through Lens Detector (TLD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13
TLD Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13
Secondary Ion / Electron Detector (ICE). . . . . . . . . . . . . . . . . . . . 5-14
ICE Detector Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-14
ICE & ETD Collection Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . 5-14
Infrared CCD Camera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-14
SEM Imaging Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
Final lens modes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
Electron source modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
Beam deceleration mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
Detection Principles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
Beam Deceleration Applications . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Beam Deceleration Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Beam Deceleration Mode Imaging Procedure . . . . . . . . . . . . . . 5-18
Capturing and Handling Single Image . . . . . . . . . . . . . . . . . . . . . 5-19
Image types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
Digital File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
Saving / Opening / Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
Image Capturing Procedure. . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
Image Printing Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
Recording Movies (Saving Multiple Images) . . . . . . . . . . . . . . . . 5-22
Movie TAB Preferences Dialogue . . . . . . . . . . . . . . . . . . . . . . . . . 5-22
Timer module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
File module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
Record Movie . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-24
Record Movie Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-24
FEI Movie Creator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25
File Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25
Databar Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26

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 Table of Contents

Preview (tab) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-27

Playing a Movie . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28
Stage Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-29
Eucentric Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-29
Setting Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
Software Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
Map tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
Coordinates tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-33
Tilt Correction tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-34
Software Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-35
Bulk tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-35
Flip tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-35
Hardware Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-36
Manual User Interface (MUI) . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-36
Joystick . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-36
Stage Related Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-37
Stage Movements – Keyboard Shift . . . . . . . . . . . . . . . . . . . . . 5-37
Stage Movements – Track. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-37
Stage Movements – Get . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-37
xT Align Feature…. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-38
Scan Rotation Align Feature . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-39
Compucentric Rotation (F12). . . . . . . . . . . . . . . . . . . . . . . . . . . 5-40
User Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-40
Scan Rotation (Shift + F12) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-43
Sample Navigation / Navigation Montage.... . . . . . . . . . . . . . . . 5-43
Navigation Alignment... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-44
Nav-Cam (in-chamber) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-45
Capturing Navigation Image Procedure . . . . . . . . . . . . . . . . . . . . 5-45
Loadlock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-46
Loadlock Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-46
Sample Height Gauge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-47
Exchanging Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-48
Loading sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-48
Unloading sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-48
Loadlock Software Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-49
Loadlock Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-49
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-49
Multiloader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-51
Loading / Unloading General Remarks. . . . . . . . . . . . . . . . . . . . . 5-51
Loading Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-51
Unloading Cartridge. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-52
Measurement and Annotation Functions . . . . . . . . . . . . . . . . . . 5-53
Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-53
Property Editor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-53
Shape Creating . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-54
Shape Editing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-54
Patterning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-55
Pattern Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-56
Tool Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-56
Basic and Advanced tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-59
Progress Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-60
Selective Mill Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-60
Progress area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-61
End Point Monitor (EPM) Module . . . . . . . . . . . . . . . . . . . . . . . . . 5-62
iSPI Tab 
(intermittent Switching between Patterning and Imaging) . . . . . 5-62
Monitor Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-62

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Table of Contents

The Settings Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-63

Gas Injection Module (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-64
Setting up the GIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-64
Application Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-65
Application Files Editing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-65
Plasma Cleaner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-68
Sample Cleaning Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-69

Chapter 6 Maintenance
Cleaning Procedures Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
List of Applied Cleaners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Cleaning Column Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Materials and Technique . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Cleaning Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Stage maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Stage mechanics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Cleaning Stage parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Specimen Holders. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Cleaning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Scroll Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
Periodic check. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
Compressor and Pneumatics System (option) . . . . . . . . . . . . . . . 6-6
Condensate Draining procedure . . . . . . . . . . . . . . . . . . . . . . . . . 6-6

Chapter 7 System Options

Optional Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
Annular Scanning Transmission Electrons Microscopy Detector 
(STEM II). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
Holder Arm Installation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
Inserting and Retracting STEM II Detector . . . . . . . . . . . . . . . . . 7-3
Settings for STEM II Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
Directional Backscattered Detector – 
Concentric Backscattered Detector (CBS) . . . . . . . . . . . . . . . . . . . 7-5
Detector Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
Inserting and Retracting CBS Detector . . . . . . . . . . . . . . . . . . . . 7-5
Obtaining an Image in BSE Mode. . . . . . . . . . . . . . . . . . . . . . . . . . 7-6
Retractable Detectors Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-6
External Current Measurement (Keithley Picoamper Meter) . . . 7-7
Fast Beam Blanker. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-8
Multi Stub Holder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-8
Torx Drivers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-8
I-Beam Charge Neutralizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-9
Finding the Optimal Operation Range . . . . . . . . . . . . . . . . . . . . . 7-9
Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-10
Nav-Cam (chamber door mounted) . . . . . . . . . . . . . . . . . . . . . . . 7-11
Capturing Navigation Image Procedure . . . . . . . . . . . . . . . . . . . . 7-11
Quick Loader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
General description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
Loading rod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
Gate valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-14
Sample Carrier, Sample Gauge and Stage Adapter . . . . . . . . . 7-14
Installation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-16

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 Table of Contents

Loading position. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-16

Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-17
Loading a sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-17
Rod Loading Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-17
Unloading a sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-18
Loading/Unloading - vented microscope chamber . . . . . . . . . . 7-18
CryoMAT Loader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-19
1. Gas Flow Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-20
2. Heat Exchanger and LN2 Dewar . . . . . . . . . . . . . . . . . . . . . . . 7-20
Water Trap. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-21
Lowering the Heat Exchanger into the Dewar . . . . . . . . . . . . . . 7-21
Removing the Heat Exchanger from the Dewar . . . . . . . . . . . . 7-21
4. Cold Trap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-21
5. Cryo Stage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-22
Cryo stage components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-23
Cryo Sample Carrier and Cryo Stubs . . . . . . . . . . . . . . . . . . . . 7-23
6. Cryo Heater & Sensor Controller . . . . . . . . . . . . . . . . . . . . . . . 7-24
Temperature Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-24
Operating the CryoMAT Loader . . . . . . . . . . . . . . . . . . . . . . . . . . 7-25
Mounting the Sample. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-25
Cooling Down the Sample (First Time Operation in Session) . . 7-25
Balancing the Flow Rate Versus Temperature . . . . . . . . . . . . . 7-25
Sample Exchange / Removing . . . . . . . . . . . . . . . . . . . . . . . . . 7-26
Finishing CryoMAT Loader Operation . . . . . . . . . . . . . . . . . . . . . 7-26
Daytime Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-26
Overnight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-26
CryoCleanerEC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-27
Parts and Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-27
Flanges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
CryoCleaner Operation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
Dewar Vessel Refilling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
Removing Nitrogen Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-29
Baking Nitrogen Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30
Replacing Nitrogen Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30
Spare Vessel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30

CONFIDENTIAL FEI Limited Rights Data C-vii

Table of Contents

C-viii FEI Limited Rights Data CONFIDENTIAL

1 SYSTEM OVERVIEW

User Manuals

FEI MICROSCOPE SYSTEMS SAFETY MANUAL

It provides important information required during operation and
maintenance for a product and personal safety.
Be sure to read at least this manual (which is delivered both as the PDF
file and as the printout).

USER OPERATION MANUAL

The User Manual is delivered in the electronic PDF file only. However, it
is possible to print parts of the manual if this is desired.
It is recommended to read the appropriate User Manual section before
operating any of the microscope function. Most importantly, you should
locate the topics necessary to operate the microscope in the proper way
to safely achieve the best results.
The manual is divided into the following chapters:
1. System Overview (this chapter) 
gives overview of the user manuals and system capabilities.
2. System Control 
describes the system hardware (interface elements, vacuum system,
system states, Equipments).
3. Software Control 
describes the interface that sets and controls system operation,
giving the function of each tool, menu item and control page.
4. Alignments 
explains how to align the equipment to achieve the optimal
performance.
5. Operations 
gives procedures for how to use the system features.
6. Maintenance 
gives allowed step by step cleaning and maintenance procedures.
7. System Options 
explains relevant options that are integrated into or accessory to the
system.
In the PDF file, you can take advantage of the searching and navigation
possibilities. The following conventions are observed:
• Some software functions use shortcuts, which are given beside the
heading in the brackets (for instance: Save (Ctrl + S)) and in the Help
menu / Keyboard Shortcuts… (see Chapter 3).
• A reference to the specific software element is highlighted in bold. For
instance: “Clear the Stage module / Coordinates tab / Z coordinate
check box.”

CONFIDENTIAL FEI Limited Rights Data 1-1

System Overview: System Capabilities

System Capabilities

The FEI® Helios™ NanoLab™ 450 / 450S / 450 ML / 650 / 600i

DualBeam™ systems integrate ion and electron beams for FIB and SEM
functionality in one machine. Users can switch between the two beams
for quick and accurate navigation and milling. Convergence of the SEM
and FIB at short working distance allows precision “slice-and-view”
cross-sectioning and analysis at high resolution.
FIB/SEM DualBeam systems provide an expanded range of capabilities
not possible with separate FIB and SEM tools:
• Electron beam high-resolution imaging of FIB cross sections without
eroding the feature of interest.
• Real-time cross-section electron beam imaging during FIB milling.
• Focused electron beam charge neutralization during FIB milling.
• Focused ion beam charge neutralization during SEM imaging.
• High resolution elemental microanalysis of defect cross sections.
• Sample surface imaging with the electron beam during navigation
without erosion or gallium implantation from the ion beam.
• TEM sample preparation with in situ conductive coating.
The Tomahawk™ ion column provides fast, precise milling and high-
resolution imaging of the sample surface.
The Elstar electron column takes advantage of FEI’s most advanced
Hexalens™ design for ultimate image resolution at low beam energies. It
offers nondestructive imaging capability at a working distance optimized
for ultrahigh resolution and can display samples magnified over 500
000× in mode 1 and > 2 500 000× in mode 2.
The Helios NanoLab was designed for imaging nanostructures of any
material (man-made, biological, natural), particularly in the area of:
• Nanoelectronics,
• Process yield engineering,
• Biology.
The system was designed for:
• Data storage
• Process yield engineering
• Etching
• Lithography
• Metal and other materials deposition
• Fabrication of micro- and nanostructures
The instrument provides optimum throughput, resolution and automation.

1-2 FEI Limited Rights Data CONFIDENTIAL

 System Overview: System Capabilities

SYSTEM PERFORMANCE
The main instrument components used for imaging of the samples are:
• Electron / Ion source 
The beam of electrons or ions (particles) is emitted within a small
spatial volume with a small angular spread and selectable energy.
• Lens system 
The beam enters the lens system consisting of several
electromagnetic or electrostatic lenses and exits to hit the specimen
surface.
• Scan unit 
The scan generator signal, fed to the deflection systems, moves the
beam in a raster pattern over the specimen area. This signal,
modulated by the detection system signal produces the onscreen
imaging of the specimen surface.
• Detection unit 
Particles striking the specimen react with atoms of the sample surface
in various manners:
– The electron beam produces electrons and photons (X-rays). 
– The ion beam produces ions, electrons and photons (X-rays).
The detector system picks up the particles or photons, converts them
into an amplified electrical signal which is then sent to the control PC
and displayed on the monitor.

FIGURE 1-1 COLUMN SCHEMATIC OVERVIEW

Electron / Ion
Source

CONDENSER LENS SYSTEM

LENS(ES)
SCAN UNIT

DEFLECTION
SCAN GENERATOR M
SYSTEM

FINAL LENS

R
TO
T EC DETECTION UNIT
DE

SPECIMEN

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System Overview: System Capabilities

Computer Control
The xT microscope Server and xT microscope Control (User Interface)
software integrate SEM and FIB functionality within a Windows XP™
operating environment.
These software consist of programs defining specific instrument settings
for particular applications, ensuring reproducibility of complex procedures
(for instance imaging, management of image capture, storage, and data
output devices etc.). They also control instrument hardware (the column,
detector(s), stage, EDX, vacuum functions etc.).

Vacuum System
The entire particle path from gun to specimen must be under vacuum so
that the particles do not collide with air molecules.
Various levels of vacuum are necessary, so a Turbo Molecular Pump
(TMP) backed by a scroll pre-vacuum pump (PVP), obtains the
necessary specimen chamber pressure.

Stage
The Helios NanoLab 450 / 450S / 450 ML / 650 / 600i has a computer-
controlled high-accuracy five-axis stage for small samples. It offers
precision specimen computer controled manipulation and automation of
all axes for overall spatial orientation on highly repetitive or extremely
irregular samples.
Specimen exchanges take place through a chamber door which exposes
the specimen stage when opened or through the LoadLock. The
exchange takes a few minutes, with the Loadlock an exchange could be
much more faster. Software and interlocks protect the system against a
damage and users against an injury.
The Multiloader is a specimen exchange unit for the modified Flip stage.
The Flip stage contains one cartrige for attaching TEM samples.
The Helios Nano Lab 650 chamber, stage, and wafer holder
accommodate wafers up to 6", or other devices, in a high-vacuum
environment.

Image Viewing and Capture

Because the amplified detector signal is displayed synchronously with
the beam scanning, there is a correspondence between brightness of an
image point on the monitor screen and the signal detected at the
corresponding point on the specimen.
Magnification is the ratio of the size of the viewing monitor screen to the
size of the area scanned on the specimen. Higher magnification is
achieved by reducing the size of the area scanned on the specimen.

Beams Control
DualBeam systems ideally position the point of interest for simultaneous
ion beam cross-sectioning and electron beam viewing. Separate scan
generators for the two beams permit coupled or independent scan
patterns and magnifications.
Imaging while milling aids in defining milled features. Immediate electron
beam images of cross sections are possible without stage motion or
sample transfer. Immediate highresolution SEM imaging after FIB milling
also prevents exposure of milled cross sections to atmospheric
contaminants.

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 System Overview: System Capabilities

Gas Injection System (GIS)

Multiple FEI GIS (option) can be installed for material deposition in
conjunction with either electron or ion beam pattern definition. Electron
beam-induced deposition offers the advantage of not sputtering the
deposited material or implanting gallium FIB source ions simultaneously.
The GIS can also contain etching precursor for fast material removal with
minimal redeposition, preferential etching of cross-section surfaces prior
to SEM imaging, and rapid milling of TEM sections.
Several GIS chemistries can be installed on the instrument, depending
on a system configuration. This self-contained apparatus allows the
material to be contained entirely within the vacuum system for simple,
flexible, and safe operation.

Analysis Capability
Convergence of the SEM, FIB, and X-ray detection system (e.g. EDX –
Energy Dispersive X-ray) (option) at short working distance allows
precision “slice-and-view” cross-sectioning and chemical analysis at high
resolution of surface and subsurface features.
Various vendor options are compatible with the instrument.

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System Overview: System Capabilities

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2 SYSTEM CONTROL

Interface Elements

SOFTWARE v5.1.X
The software control contains graphic applications within Windows XP™
operating environment. xT microscope Server starts and stops basic
microscope functions. It allows to open and close the xT microscope
Control software (UI – user interface or sometimes xTUI within dialogue
boxes) which controls all system functions including detection and
analysis, scanning, image gathering, manipulation and output,
magnification, etc.
All user account levels created via FEI User Management software
ensure for the particular users admission to both the operating system
Windows XP and the xT microscope Control software. The hierarchy of
user account levels consists of the following:
• FEI Account Administrator
• FEI Supervisor Users
• FEI Microscope Users
• FEI Non-active Users
For information on Logging on and Logging off, the start-up of the system
and all the features of the user interface elements see Chapters 3 and 5.

HARDWARE
The system is computer controlled and as such has a Microscope
Controller which must be turned on (use the power button on the PC) to
operate the microscope by means of the software. The Electrical
Console powers components of the Microscope Console (vacuum,
gun, column, stage...). The support computer can hold some other
software utilities. The switch box switches the keyboard and the mouse
to either of the two computers. The control software facilities and data
are displayed graphically on the LCD monitor and are superimposed
around and on the image. The other LCD monitor is used either as an
extended desktop of the Microscope controller or as the support
computer monitor. To control software utilities one can use a keyboard,
mouse, joystick or the Manual User Interface.

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System Control: Interface Elements

Microscope Console Control Panel

The console / system power is activated by pressing the front panel
Power button located on the microscope console. This switches the
sub-systems on and allows the interface and communication with the
microscope controller. Most of the functions are activated via the
software control. The power button green light indicates the Full
Operation state, the orange light indicates the Standby state.

FIGURE 2-1 SYSTEM CONTROL PANEL POWER BUTTON

ON

Standby

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 System Control: Vacuum System

Vacuum System

Within the system are the following vacuum sections:

• Electron source
• Electron column
• Ion source
• Ion Column
• Specimen chamber – Loadlock
In operation the electron column is always pumped to high vacuum. The
specimen chamber is at the pressure required for the given state.
All valve and pump operations are fully automatic.

FIGURE 2-2 HELIOS NANOLAB VACUUM SYSTEM

Legend: 

BPV . . . . Bypass Valve

CCG . . . . Cold Cathode Gauge
CIV . . . . . Column Isolation Valve
CLV . . . . . Chamber LoadLock Valve
CVV . . . . Column Venting Valve
GIV . . . . . Gun Isolation Valve
IGP . . . . . Ion Getter Pump
Ion DP . . . Ion Column Differential Pumping
LVV . . . . . LoadLock Venting Valve
LRV . . . . LoadLock Roughing Valve
NAV . . . . Nitrogen Admitance Valve
PIGB . . . . Pirani Gauge Buffer
PIGL . . . . Pirani Gauge LoadLock
PVP . . . . Pre Vacuum Pump
RV . . . . . . Roughing Valve
TMP . . . . Turbo Molecular Pump
TVV . . . . . Turbo Venting Valve
VV . . . . . . Venting Valve

VACUUM STATUS
The vacuum status controls are in the Vacuum module. The Pump
button starts pumping for the operating pressure and the Vent button
starts venting for a sample exchange (see Chapter 3).
In the Status module at the bottom of any page the actual vacuum status
is represented by the colored icon, which may have three possible colors
with the following meaning (see Chapter 3):
• Green: PUMPED to the desired vacuum mode (see below)
• Orange: TRANSITION between two vacuum modes 
(pumping / venting)
• Grey: VENTED for sample exchange
In the Pumped status the chamber is in high vacuum and the pressure
should be in the range 10-2 - 10-5 Pa (10-4 - 10-7 mbarr).
The actual specimen chamber pressure is displayed in the Status
module / Chamber Pressure field.

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System Control: Vacuum System

Pump button
When the Pump button is clicked and the status is Vented the system
pumps to high vacuum mode and the Pump button gets highlighted in
and not accessible.
When the Pump button is clicked and the status is Transition (venting),
the venting procedure stops and the system immediately starts to pump
to the actually selected vacuum mode.

Vent button
When the Vent button is clicked and the status is Pumped, the
confirmation dialogue appears. After confirmation, the system switches
off the detectors voltage, high voltage supplies, vacuum pumps and uses
the appropriate valves to vent the system.
The Vent button is highlighted and not accessible. After a specified
venting time the venting valve closes and the vacuum status should
indicate Vented. The chamber door could be opened and the button is
enabled again.
When the Vent button is clicked and the status is Transition (pumping),
the dialogue appears. After confirmation, the pumping procedure stops
and the venting procedure starts.
When the Vent button is clicked and the status is Vented, the dialogue
appears. After confirmation, the venting valves re-open for the specified
venting time and then the valves close.

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 System Control: System States

System States

There are several system states:

1. Complete Shutdown – service and emergency reasons
Complete shutdown should be performed only if absolutely necessary
and for the shortest possible time, so as to recover the column
vacuum without the necessity of a system pump.
The shutdown procedure brings the system to a non-powered state,
where the vacuum in the specimen chamber is no longer supported
by running pumps (PVP and TMP are switched off). All valves are
closed, so the system remains in the last vacuum state. The TMP will
slow down gradually and the chamber and column vent finally. The
specimen and/or LoadLock chamber could not be accessible unless
they are vented before the complete shutdown.
The vacuum in the electron gun and column is still supported by an
independent Battery Supply Unit for a limited amount of time (~ 9
hours). After that the system vents completely and the service
procedures are needed to restore the system.
Caution! 
The emission characteristics of the source are dependent on the
shape of the tip. When the source is turned off, it cools. Reheating the
source during startup changes the shape and emission
characteristics, requiring the column to be re-aligned.
2. Standby – not using the system for a few days or during service
This mode is only available for supervisor users. The electronics
racks are powerless except for the E-column source, vacuum pumps
and optionally Microscope Controller. The latest vacuum state is
preserved. Returning to full operation takes a few minutes.
3. Overnight – not using the system for a few hours, e.g. overnight
When not using the SEM, switch off the electron beam (accelerating
voltage). To decrease energy consumption, switch off PC’s also.
Returning to full operation takes from a few seconds to a few minutes,
depending on whether the microscope controller is switched off.
4. Full Operation – working
TABLE 2-1 SYSTEM ON / OFF OVERVIEW

Complete Full
Instrument Unit Shutdown Standby Overnight Operation
Microscope console Off Partly Off On On
PC’s (Microscope Controller &  Off On / Off On / Off On
Support Computer)
Software (xT microscope Server & Off Off On / Off On
xT microscope Control)
Vacuum Off On On On
Electron Beam (HV) Off Off Off On

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System Control: System States

TABLE 2-2 STARTUP PROCEDURE GENERALLY

Transition Action to reach Full operation state

from 1) Connect compressed air and nitrogen (if present),
Disconnected cooling water and the power cord to the microscope
console.
from 2) Push the power button on the microscope console
Complete front panel.
Shutdown 3) Switch on the PC’s. The operating system
Windows XP loads(a) and displays the appropriate
icons on the monitor desktop.
4) Double-click the xT microscope Server icon to
start the software (all device bullets should be green).
5) Click the Start button to start the server.
6) Click the Start UI button (if not started
automatically) to start the xT microscope Control
software.
7) Enter your Username and the Password (a) into
the XTUI Log On dialogue to activate the Microscope
Control software (b).

8) Switch on the IGP’s and the Emitter by the

Alignment 5 - Emitter Startup (see Chapter 4).
Note: 
When IGP’s start fails (long time of interruption) call
FEI Service Engineer.
9) Pump the chamber to reach the Pumped status.
10) Click the Column module / Beam On button
(turns to yellow) to start the beam.
from Standby Run the steps from No. 2) to 7) and follow with steps
No. 9) and 10).
Note: 
Skip steps which are allready done.
CAUTION! 
Wait at least 10 sec after the system has got to the
standby mode before you start the system again by
pressing the microscope console power button.
from Run the steps from No. 3) to 7) and follow with the
Overnight step No. 10).
See Chapter 5 to set desired imaging conditions.

Note: 
a)
Once you have your FEI Microscope User / FEI Supervisor User
account set up via FEI User Management software by FEI Account
Administrator (see Chapter 3), you can use your name and password
(case sensitive) to access both Windows XP system and the
xT microscope Control software.
b) The stage needs the home stage procedure (see Chapter 3) to be
completed before full operation of the UI is possible. For this purpose a
dialog is displayed onscreen after the Log-on procedure. If the procedure
is not completed now, one can perform it by selecting the Stage menu /
Home Stage (Shift + F3) later (when the imaging is on).

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 System Control: System States

TABLE 2-3 SHUT DOWN PROCEDURE GENERALLY

End state Action from Full Operation on

to Overnight 1) Click the Column module / Beam On button to
switch off the beam. (c)
2) Select (d) the File menu / Log Off… to log off the
present user and to provide the Log On dialogue for
entering another one.
Note: 
Optionally stop the xT microscope Server and
shutdown the PC’s to reduce the power consumption.
to Standby Run steps No. 1) and 2).
3) Click the xT microscope Server window / Stop
button.
4) Click the xT microscope Server window /
Standby button.
5) Switch Off the PC’s and the monitors.
to Complete 6) Switch off the Emitter (see Chapter 5).
Shutdown 7) Vent the specimen chamber
Run the steps from No. 2) to No. 5) on.
To 8) Disconnect the power cord, compressed air,
Disconnected nitrogen (if present) and cooling water.
(e)
Note: 
Electron source and column vacuum is supported for
another about 8 hours by an separate IGP’s battery
supply unit.

Note:
c)It is strongly recommended to always leave the chamber in the
pumped state when the instrument is not used.
d)
Waiting for a new user leaves the status of the xT microscope
Control software non-operational and only the xT microscope Server
software is active. Therefore changing an user does not require Logging
off / Logging on at Windows XP level, but just restarting the UI level.
e)
Disconnecting the power cord brings the system to a non-powered
state. All valves are closed, so the electron column and specimen
chamber areas are not automatically vented, but the vacuum in the
instrument is no longer supported by running pumps. This should only be
carried out by an FEI service engineer. Normally it is used for a system
transportation or for service actions, like repair of essential systems (e.g.
power supplies).

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System Control: System States

POWER OFF
A power failure is never good for the system. Take sufficient measures to
avoid power failures. If a power failure occurs while the instrument is fully
operational, the microscope comes down to a safe state and the
following happens:
• The accelerating voltage is switched off abruptly.
• Electron emission is switched off.
• The vacuum in the instrument is no longer supported by running
pumps. All valves are closed, so the vacuum in the column and
chamber is not completely lost.
Caution! 
Switching off the console when Emitter is on is not optimal and
sparing way for the emitter. User should use the Shutdown System
button only in case of emergency need.
• The microscope and support PC’s are switched off, the momentary
adjustments of all system parameters (accelerating voltage,
magnification, stage positions etc.) are lost if they were not saved.
Note: 
If the power failures occur occasionally it is recommended to use the
microscope Uniterruptible Power Supply (UPS - option).

Emergency Off
This is similar to that which would happen after a MAINS power off. Here
are several possibilities how to quickly switch off the electrical power
completely in case of emergency:
1. Push the red EMERGENCY (EMO) button (option - see the Safety
Manual).
If the button is not installed proceed as follows:
2. Switch off the breaker switch labeled MAINS S1 at the cabinet back,
which is placed at the very right side in the row.

FIGURE 2-3 MAINS SWITCH BOARD

If this is not easily accessible:

3. Turn off the mains wall switch (if present), and / or disconnect the
mains plug from the mains socket.

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 System Control: Equipments

Equipments

DETECTOR TYPES AND USAGE

The Detectors menu shows all installed detectors, the selected one has
a tick mark next to its label. The system remembers the last detector
used for a particular vacuum mode and its Contrast & Brightness
settings.
Note: 
If any detector not compatible with the actual mode which is selected, the
imaging quad cannot be activated.
TABLE 2-4 ALL DETECTORS TYPES

Detector Name UI Tag Detected Signal Note

Everhart-Thornley ETD SE / BSE S
CCD camera CCD light, infra-red light S
Through Lens TLD SE (tunable energy)  S
BSE
External EXT detector-dependent O
Secondary Ions Detector ICE Electron beam: SE / BSE  S, O (650 / 600i)
Ion beam: SE / SI
Concentric Backscattered CBS BSE O
Nav-Cam S, O (600i)
Annular STEM STEM II TE O

SE = secondary electrons, BSE = back scattered electrons, 

TE = transmitted electron, SI = secondary ions 
S = standard, O = optional
For settings and handling of particular detectors see Chapters 5 and 7.

PLASMACLEANER
Helios NanoLab 450 / Helios NanoLab 450 S / Helios NanoLab 450 ML / 
Helios NanoLab 650 / Helios NanoLab 600i - option
The plasma cleaner decrease the hydrocarbon molecules contamination
level (see Chapter 5).

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STAGES
For settings and handling the stage and its accessories see Chapter 5.
The stage has the X, Y, Z, Rotation and Tilt movements motorised and
is fully eucentric. All movements are read out on the screen, under the
software control. The software control is an integrated part of the xT
microscope Control software.

FIGURE 2-4 HELIOS NANOLAB 450S

X-section Sample Holder

This tool enables to observe sample cross sections (wafers etc).

FIGURE 2-5 X-SECTION SAMPLE HOLDER

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 System Control: Equipments

Loadlock
Helios NanoLab 450 / Helios NanoLab 450 S / Helios NanoLab 450 ML
The Loadlock enables a specimen exchange through the pre-pumped
Loadlock chamber, eliminating the need to vent and evacuate the entire
specimen chamber.

FIGURE 2-6 LOADLOCK

Multiloader
Helios NanoLab 450 ML

FIGURE 2-7 MULTILOADER /

Nav-Cam (in-chamber)
Helios NanoLab 450 / Helios NanoLab 450 S / Helios NanoLab 450 ML

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System Control: Equipments

Stage movement limits

The motorised movements of the stage can be operated under the
software control for more advanced location mapping. This includes
Shift, Get, Track and the Stage module functionality. A live image can
be repositioned either by the stage movement or by the Beam Shift (see
Chapter 5).
Note: 
When moving the stage or tilting the specimen, the magnification may
need to be reduced not to move the feature of interest off the screen.

FIGURE 2-8 STAGE MOVEMENT SCHEMA

TABLE 2-5 STAGE FEATURES AND LIMITS

Item 100 × 100 mm Stage 150 × 150 mm Stage Note

X from -50 to +80 mm -75 +75 mm
Y -50 +50 mm -75 +75 mm
Z 0 + 20 mm 10 + 20 mm internal + external
R 360° 360° continuous
T -10° to +60° -10° to +60° Check the sample size
Eucentric Position Electron: WD = 4 mm Electron: WD = 4 mm
Ion: WD = 16.5 mm Ion: WD = 16.5 mm
Clamp No No
Maximum sample 200 g 500 g Loadlock, for all tilt angles
weight
500 g 1 500 g without Loadlock, at Tilt = 0°

Caution! 
The positive Z value direction depends on the Link Z to FWD status (see
Chapter 5).
Caution! 
Stage tilt is limited by the specimen size. Beware of hitting the objective
pole piece!

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3 SOFTWARE CONTROL

This chapter describes the functionality of each part of the user interface.

SOFTWARE INTERFACE
The software control contains graphic applications within Windows XP™
operating environment. xT microscope Server starts and stops the
basic microscope functions.
It makes possible to open and close the xT microscope Control
software (UI – user interface or sometimes xTUI in the dialogue boxes)
which controls system functions including imaging, image and movie
gathering / manipulation / output, detection and analysis, scanning,
magnification, stage navigation, chamber and column pressure, etc.
All user account levels are created via FEI User Management software,
ensuring for the particular users admission to both the operating system
Windows XP and the xT microscope Control software.

OTHER SOFTWARE AND HARDWARE

Call Customer Service for advice before installing software or hardware
that is not required for system operation. Other software, such as screen
savers or hardware network cards, may corrupt the xT microscope
Server / Control software under some circumstances and may invalidate
warranty.
For more detailed information about Windows XP, refer to the Microsoft®
Windows™ User’s Guide shipped with your system.

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Software Control: Software Interface Elements

Software Interface Elements

ICONS
Icons are small symbols indicating a specific software application.
Double-click the icon to activate the program.
There are also functional icons in the toolbar for selecting some
software functions quickly. Clicking causes it to press in and activate,
clicking it again or clicking another one (depending on a particular case)
causes it to spring out and deactivate.
Some functional icons have additional down-arrow next to the right side.
Clicking the arrow displays a pull-down menu with choices, while clicking
the icon performs a particular function (cyclic changeover of choices,
setting the default parameters etc.).
There are also some informational icons in the status field, for
instance, that indicate some particular system status.

TOOL-TIPS
This functionality activates when the cursor is left over an item on the
user interface for more than two seconds. A short explanation of the item
appears until the cursor is moved away from the item.

PULL-DOWN MENUS
The microscope uses menu-oriented software; you perform functions by
choosing items from the Menu bar. The Menu bar selections contain
pull-down menus that display grouped listings of available commands or
settings. Some menu items are shown in grey and cannot be selected
because of the system immediate condition.
Pull-down menu selections followed by the ellipsis (…) indicate, that a
dialogue box will display (the same behaviour occurs when the selection
is a command). Selections with a right arrow indicate that an additional
submenu of choices will display. If a selection is a parameter value, the
new value is updated immediately and a check mark appears in the pull-
down menu.

Using the Mouse

The click / right-click / wheel-click represents click with the left / right /
wheel mouse button on the item throughout this manual. The press /
right-press / wheel-press means clicking and holding the mouse button
during the action.
Press the menu bar item, drag the cursor down to a desired selection
and then release the mouse button.

Using the Keyboard

Press ALT + the underlined letter (for example, ALT + F for the File menu),
and then select from the choices by clicking it or by hitting the Enter button
after its location with the up / down (left / right for submenus) arrow keys.
Some often-used commands can quickly be activated with the use of
shortcut keys (a combination of simultaneously pressed keys) at any time.
This possibility is given by a particular button combination on the right
side of the pull-down menu adjacent to the appropriate command.

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COMMAND BUTTONS
carry out or cancel functions. They press in when clicked and some
change color to show the corresponding function activity.
Command buttons have labels that describe the actions performed by
clicking them. The most common ones, which are typically used in
dialogues are:
• The OK button applies all changes made in the dialogue and closes it.
• The Finish button saves new settings, ends the procedure and closes
the dialogue.
• The Save button saves new settings at that point without closing the
dialogue.
• The Apply button saves and applies new settings at that point without
closing the dialogue.
• The Cancel button discards all changes (made from the last save) and
closes the dialogue. It has the same effect as closing the dialogue with
the cross (Alt + F4).
• The Next button moves an user to the following dialogue after
necessary settings have been done.
• The Previous button moves an user to the previous page when
settings need to be changed.

LIST BOXES
contain available choices, such as screen resolution, magnification
settings, etc. Click the List box to roll down a list of available values, then
click the desired one. The drop down list automatically closes and
displays the new value as the actual one. The change of the setting is
immediate.

PROPERTY EDITORS
group list of related parameters and their values. The editable
parameters have a white background, the fixed parameters are shaded.
An user should click in the Value side of the relevant property Name and
then select its value from the drop down list or enter it using a keyboard.

EDIT BOXES
let you input text information (such as passwords, labels or precise
numbers) using the keyboard. Some edit boxes, which are not part of a
dialogue, require to confirm the input by pressing Enter. If you press Esc
before leaving the edit box, its previous value is restored.

RADIO BUTTONS / CHECK BOXES

Within a group of related round Radio buttons, only one selection can
be made active at any time by clicking the individual round box.
A single one or a group of square Check boxes can be ticked / cleared
by clicking the individual square box.

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Software Control: Software Interface Elements

ADJUSTERS
allow to change parameters, such as contrast, brightness, gamma etc. in
a continuous way by pressing and dragging the middle adjuster or
clicking in the grey bar. They always have a label in the upper left and
right corners for readout information. Double-click the value in the upper
right corner enables to enter a precise value (and the unit in particular
cases) using the keyboard.

Exponential Adjuster
This is an exponential response adjuster – the further from the center is
the large adjuster button pulled, the larger is the relative change. The
adjuster button always snaps back to the center of the slider.
The middle adjuster button is for coarse adjustments, while the end
arrows are for fine adjustments (single step increments).

Linear Adjuster
Some adjusters have linear response like the small adjuster placed
below the exponential one has. Its button position always corresponds to
the actual parameter value within an available range.

Preset Adjuster
This kind of adjuster is used for values that have both a continuous
range, a list of presets and direct value editing to achieve total control.
The button on the left side of the adjuster toggles between modes:
• Drop-down list: 
clicking the -/+ buttons on the right of the drop-down menu steps
through the pre-set values Up / Down in the list, but only shows one
value in the text area. Clicking the down-arrow rolls down the whole
list of values. If the list extends further than is visible, a scroll bar
appears. Clicking a value in the list enters it as an actual value in the
text area displayed at the top. 
Double-clicking a value in the text area enables to edit it.
• Adjuster mechanism: 
The adjuster has a fine control (see above).

Spinner
allows to change a parameter in an incremental way from a list of pre-
defined values by clicking on an arrow.

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2D CONTROLS
are represented by an X-Y box. The position of the crosshair
corresponds to the actual parameter value with respect to its full range
being represented by the perimeter of the box.
Pressing anywhere inside the box changes the active quad cursor to the
four-ended arrow and positions it to the screen point corresponding to
the actual control value (minimum in the middle of the screen and
maximum at the edges). It can be moved in four directions. Pressing
directly on the X / Y axis changes the active quad cursor to the two-
ended arrow, which can be moved in the corresponding direction only. To
fix the values, release the mouse button.
The right-clicking over the 2D box opens a dialogue with choices:
• The Coarse / Fine sets the mouse sensitivity – long / short mouse
path necessary for the full range.
• The Adaptive Sensitivity adjusts the mouse control response to be
the same at any magnification.
• The Zero brings the control value to zero and the cursor to the center
of the box.
• The Back brings the control value one step back (only one step is
remembered).
• The Clear Memory clears condition values, which have been
remembered automatically during the considered 2D control use.
These remembered values are used to estimate new values, which
have not been remembered yet.
The menu may contain less or some other functions that are actually
available for the particular parameter. Selecting the corresponding menu
item activates the function.

MODULES
visually combine various software elements, which are related into a
labeled group. Complex software elements like UI pages or dialogues
are typically composed of modules.

DIALOGUES
appear when the system needs more information from you before it can
carry out a command, or want to give you some important actual
information. Some dialogues do not let you access other functions until
you close them, other ones let you perform other tasks while they remain
onscreen and active (for example, the Preferences dialogue can remain
opened while performing other tasks).

TABS
In modules or dialogues containing more interface elements than would
fit into the limited area the Tabs are used. These related elements are
split into the groups (sections) and each one is supplemented with the
labeled Tab. Clicking the Tab brings it to the foreground displaying the
corresponding group of interface elements.

PROGRESS BARS
indicate progress of a long ongoing procedure over time. It is often
displayed in a dedicated dialogue.

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Software Control: xT microscope Server Software

xT microscope Server Software

The xT microscope Server application starts and stops the software

service controlling basic microscope functions and also the user
interface (UI) software xT microscope Control.
Run the xT microscope Server (from the Windows Start menu or
double-click the icon) – the application window appears. The title bar
right-clicking opens a dialogue that offers the option to minimize the
server to the UI top bar.

FIGURE 3-1 xT MICROSCOPE SERVER WINDOW

• The Server State / UI State modules display the RUNNING or

STOPPED state of the xT microscope Server / xT microscope Control
software services. During a transition between these states
STARTING or STOPPING is displayed.
• Some Microscope module buttons change its label and behaviour
depending on the actual state.
The Start / Stop buttons start / stop xT microscope Server services. If
the xT microscope Control (UI) is running, Stop button closes it first.
The Show UI / Hide UI button calls / hides the UI main window.
The Start UI / Stop UI button opens / closes xT microscope Control
(UI) software.
The Standby button closes the xT microscope Control software (UI),
stops the xT microscope Server services and brings the console to
the Standby State (see Chapter 2).
The Advanced button displays the Administration module
containing information helpful when calling the service (specifying the
software operation / hardware function state).
- The Autorun UI checkbox: when ticked (default), the Start button
automatically starts xT microscope Control after starting the Server.

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xT microscope Control Software

xT microscope Control – also called User Interface (xTUI or UI) – is

made up of several elements which compose the main window,
displaying status and control features.
Note: 
Today the UI suports wide screen display which leads to a slightly
different appearance of some UI elements in comparison to this manual.

FIGURE 3-2 THE MAIN WINDOW

1
2
3 5

4 - Quad 1 4 - Quad 2

4 - Quad 3 6 4 - Quad 4

1. The Title bar – labels the application

2. The Menu bar – contains all operation menus and submenus
3. The Toolbar – contains functional icons for the most frequently used
microscope controls and for the fast access to the Pages
4. The Imaging area – quads with adjustable Databar
5. Pages and Modules – microscope and imaging control elements
organized into modules making up the pages
6. The Preferences dialogue – presetting of operating conditions
(displayed image is illustrative only)

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TITLE BAR
displays the application icon and name plus the standard Windows
buttons: Minimize and Close, which are enabled.

FIGURE 3-3 THE TITLE BAR

The Close button quits the xT microscope Control software (accelerating

and detectors voltages are switched off for the security reasons).

MENU BAR
displays pull-down menus across the screen below the Title Bar.

FIGURE 3-4 THE MENU BAR

Select pull-down menus from the menu bar by:

• clicking the Menu title
• Alt + hitting underscored keyboard letters + using keyboard arrows
Note: 
Some menu functions have their equivalents in the toolbar. In such
cases, the corresponding toolbar icon is shown next to the function title
in the following text.

File Menu (Alt + F)

opens File menu administrative functions:
Open…
displays a standard dialogue for opening images previously stored to a
media. Supported file formats are TIF8/16/24, JPG and BMP (see
Chapter 5). The dialogue displays, by default, the location (path) last
used to open or save files from the xTUI.
Save (Ctrl + S)
saves the image using the format, location and base of name set by the
last used Save As function in that quad. An incremental suffix with a
selectable number of digits ensures that every image is saved as a new
file, e.g. Name_001.tif, Name_002.tif, etc.
Save As…
opens a dialogue for saving images, which provides an opportunity to
change the file name and location. An image can be saved in TIF8/16/
24, JPG or BMP file format.
The dialogue displays, by default, the location and the name last used to
save / open a file in the active quad. You can choose different location,
name base or suffix, select different image format (Save as type), and
also choose whether to Save the image with / without Databar and with
/ without overlaid graphics by ticking / clearing an appropriate check
box. The settings is remembered per quad and used for the subsequent
Save actions.

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FIGURE 3-5 SAVE AS… DIALOGUE

Save All… (Ctrl + Shift + S)

opens common dialogue for saving images from each quad, providing an
opportunity to change the file names and locations.

FIGURE 3-6 SAVE ALL… DIALOGUE

Image Properties (Shift + F1)

allows an user to view parameters at which an image was captured.
Record Movie (Ctrl + Shift + M)
allows an user to make digital video files (AVI) for dynamic experiments.
The tick next to this menu item and the change of the corresponding
toolbar icon indicates the movie recording (see Chapter 5).

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Import / Export
opens a sub-menu with selection of importable / exportable items.
Selecting an item opens standard Open / Save As dialogue for choosing
location and file name. Following items can be both imported (i.e. loaded
and used – see Toolbar icon) / exported:
• The Stage Positions… stored with the use of the Stage module 
(.stg files)
• The Patterns… used in the patterning module (.ptf files) (see Chapter 5)
• The End-Point Monitor Graphs… used for milling (.epm files)
• The Scanning Presets… parameters (.scp files) (see Preferences…)
• The Quad Presets… parameters (.qps file: Beam type / Detector
type / Detector Mode / Detector contrast & brightness / Digital
Contrast / Digital Brightness)
The System Parameters… option enables to save a selection of actual
microscope settings (.par files) also including above mentioned ones.
When importing them back likewise only selected ones are loaded.
Print… (Ctrl + P)
opens the print dialogue enabling a choice of printer and settings suitable
to print an image.
Log Off User…
logs off a present User and provides the Log On dialogue for the next
microscope user. When an user logs off the system goes to a safe state:
the accelerating and detector voltages are switched off automatically.
Caution! 
Logging off an actual user does not close all microscope operations!
(See Chapter 2)
Exit
closes the xT microscope Control software (an actual user is automatically
logged off first) and leaves an user in the operating system environment. xT
microscope Server is still running and controls the microscope in operation.

Edit Menu (Alt + E)

opens some helpful functions applicable for patterns, measurements and
annotations:
Copy (Ctrl + C) / Cut (Ctrl + X) / Paste (Ctrl + V) / Delete (Del)
These functions represent commonly used operating system
functionality.
Select All (Ctrl + A)
selects all items within a selected quad.

Detectors Menu (Alt + D)

opens the selection and setting of all installed Detectors (see Chapter 5
and Cahpter 7).
Detector list
contains various detectors for the microscope operation. Detectors not
mounted or not serviceable under an actual microscope conditions are
disabled (greyed out). The selected detector for the selected quad shows
a tick next to its label.
• An 3rd party video signal can be selected, which is indicated as
“External” in the databar. Contact a FEI service person about a
connection details.

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• The CCD camera reflects the inner space of the specimen chamber.
• The Mix sets a possibility to interfuse signals from 2 or 3 detectors.

Scan Menu (Alt + C)

opens the scanning control functions:
Pause (F6)
pauses the imaging. This function is used automatically 
with Snapshot and Photo functions.
Select the Scan menu / Pause or press the F6 button or click / double-
click the toolbar pause icon to stop scanning at the end of the actual
frame / immediately.
When the quad is going to be paused at the end of 
the frame the Pause icon is pressed-in and has an orange 
background. When the quad is paused the icon remains 
pressed-in but its background reverts to normal and 
a green box surrounding two vertical green bars appears in the
corresponding quad.
Select Scan menu \ Pause item or press F6 button or click the toolbar
Pause icon to release the pause function (the icon button pops out) and
to return the scanning to the previous state. Shift + clicking the Pause
icon pauses / activates all quads with an electron imaging at once.
Snapshot ((Ctrl +) F4) / Photo (F2)
activates a preset scan (see the Preferences… / Scanning tab) 
to acquire an image. The icon could be selected by clicking the small
black arrow next to the toolbar icon.
Note: 
There are two hotkeys for the Snapshot: F4 for an electron and Ctrl + F4
for an ion imaging (not mentioned in the Scan menu). The Photo hotkey
F2 works with an active imaging beam.
Active Preset Snapshot (Ctrl + F2)
If any of six presets is activated by clicking the numbered button
(becomes yellow), image acquiring starts with corresponding
parameters. Use the toolbar expand / hide arrow to change preset
parameters. These presets could be Exported / Imported with the use of
appropriate buttons / menu items. The functionality is available only, if
activated in the Preferences… / General tab / ).
Note: 
Shift + clicking the Photo icon / active Preset Snapshot button or when
pressing Shift + F2 / Ctrl + Shift + F2 key takes electron beam Snapshot /
active Preset Snapshot from all quads at once.
Videoscope (F3)
This function shows the video signal intensity along the actually scanned
horizontal line for correcting the contrast and brightness.
Reduced area (F7)
This mode is useful when focusing and stigmating as the scan speed is
faster in the smaller area. When Reduced area is chosen, the small
green frame appears at the last used place onscreen, which could be
adjusted by pressing and draging. It is also possible to adjust scan
parameters independently on the full-frame setting.
• Moving: Place the mouse cursor over the selected area. The arrow
changes to a 4-ended arrow. Press and drag the selected area to the
desired position and release the mouse.

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• Changing the size: Place the mouse cursor over the edge of the
selected area. The cursor changes to a 2-ended arrow, either
horizontal or vertical. A corner can also be used to move two sides.
Press and drag the side out or in to obtain the desired size and
release the mouse.
When the Reduced area frame is being manipulated, it turns yellow until
released, then it reverts to green.
Full Frame (Ctrl + M)
is the default scanning mode, typical for navigation and imaging.
Spot (Ctrl + K)
When starting this mode, the beam is blanked and the scanning is
switched off. Actual beam position is represented by a green cross in all
electron quads. You can move the cross or click anywhere around the
screen to change its position.
Line
In this mode, the green horizontal line is displayed in all electron quads.
The beam scans along this line. You can move it with the mouse or click
anywhere around the screen to change its position.
External
switches to activate external control of the scanning system, such as
beam control from an EDX system. The external scanning mode is
indicated by the External label displayed in the upper right corner of all
imaging quads.
Beam Blank (Ctrl + B)
deflects the beam off axis high in the column and protects the specimen
from unnecessary exposure. When the beam is blanked the toolbar icon
is highlighted. Clicking it releases the blanker and returns the beam to
scan the specimen.
Slow / Fast Scan (Ctrl + Shift + , / .)
brings the scanning condition to the preset 
Slow (left icon) / Fast (right icon) scan value (see the Preferences… /
Scanning tab). When either of the two presets is selected the respective
icon is highlighted.
Slower / Faster Scan (Ctrl + , / .)
sets the scanning condition to the next preset Slower (left arrow) / Faster
(right arrow) value (see the Preferences… / Scanning tab). The spinner
box shows the actual dwell time, but does not enable to change or select
directly its value - the values are changed one step up or down.
Mains Lock
When ticked, the scanning (line or frame sawtooth signal) is
synchronized with the mains AC oscillations. This greatly diminishes
blurring and jittering of the electron imaging resulting in smooth image
edges at higher magnifications and slow scan conditions.
Line Integration
With this function each line scan is repeated several times (from 2 to
100) before proceeding to the next line. Signal data collected from
these passes are integrated and displayed as an actual image line.
This imaging method reduces sample charging (in comparison with
single pass with longer dwell time) and improves overall image quality.

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Scan Interlacing
This function splits an imaging area into blocks defined by the number of
lines (from 2 to 8). In the first instance the first line of each block is
scanned, then the second one etc. This imaging method significantly
reduces sample charging.
Note: 
When two above mentioned functions are active, it is represented in the
toolbar scan speed spiner with the letters LI / SI.
Live
is the default mode, leaving the imaging unfiltered for collecting raw
direct images - one frame follows another.
Average
continuously averages a specified number (2 or more) 
of frames, resulting in a better signal-to-noise ratio. This process
continues until stopped by changing the scanning condition or by
pausing the quad.
This is used mostly for fast scanning to reduce imaging noise. During
averaging, the image is updated continuously and actions such as
focusing, moving the stage, etc. can still be performed.
Note: 
The Average is set independently also for the optical window (option),
but using averaging with more than 4 frames is not recommended,
especially when moving the stage.
Integrate
allows accumulative noise reduction by true integration 
over a specified number (1 or more) of frames. This process continues
until the selected number of frames is reached and then pauses the quad
automatically. During and after image accumulation, you cannot change
the focus or perform other actions influencing the imaging.
This can be used as an alternative to slow scanning to obtain high quality
images of slightly charging specimens.
Note: 
Clicking the down-arrow next to the icon displays menu items Live /
Average / Integrate, Number of Frames enabling to select number of
averaged or integrated images (depending on the actually active Filter
Mode indicated by the icon for the selected quad). Clicking the icon itself
changes the Live / Average / Integrate mode in cycle.
The Number of Frames is set and remembered independently for the
Average and Integrate filters. Both the Filter mode and Number of
Frames is set and remembered per quad, so live and filtered imaging
can run at the same time. Settings are particular for the Reduced Area
and for the Full Frame also. The Photo function uses the Filter Mode and
Number of Frames pre-set (see the Preferences… / Scanning tab).
As the scanning could take a significantly long time period, one can
restart it from the beginning with the use of Ctrl + R keys (Restart Scan).
Alternate Electron/Ion scanning
When ticked, tha scanning alternates between the electron and ion
imaging in two separate quads after completion of each frame.
A message is displayed in affected quads. All scanning parameters are
changed during switchng the quads so it takes significantly long time
under some settings.

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Scan Rotation (Shift + F12)

activates the on-screen tool to rotate the scan field. It has no effect on
the stage movements and is solely a scan coil function used to orient the
imaging relative to a specimen feature and/or detector direction. A non-
zero scan rotation is indicated by an icon in the Status module, and its
value can be also displayed in optical quads (see Chapter 5).

Beam Menu (Alt + B)

opens the Beam menu functions:
Electron Beam / Ion Beam / CCD Camera
makes the quad or single screen active to the Electron Beam / Ion
Beam / CCD Camera (the displayed icon sequence) with respect to the
source, column, scanning, and detector settings. Only one is active at
any time, but can be operated independently for each quad.
Another possibility to change the beam for the particular quad is right or
left clicking the toolbar or image databar beam icon.
Toggle E-I Beam (Ctrl + T)
This function quickly toggles electron and ion beams to be used in the
selected quad for an imaging.
Magnification Correction
When ticked, the E-column: Magnification Correction alignment (see
Chapter 4) influences the imaging, otherwise it is not appllied. 
The “c” letter is added to appropriate databar fields (Mag, HFW) and the
“Magnification Correction” text is added to the imaging quad.
Home SEM / FIB Apertures
This function sends the SEM / FIB aperture mechanism to its home
position in case of troubles.
SEM Mode
This item opens a sub-menu with selection of three different imaging
modes, in which the electron column could be operated. They can be
selected directly from the toolbar also (see Chapter 5).
Do Not Degauss
When ticked, an automatic UHR lens degauss procedure is dissabled
because of accelerating operation (for instance during switching from
electron UHR mode to ion beam imaging).
UC On / UC Auto
Model difference: Helios NanoLab 600i does not have the UC item.
When ticked the UC-mode (UniColor mode) for the electron beam is set
on. Ticking the UC Auto switches UC-mode on automatically, when
particular conditions are accomplished (see Chapter 5).
Lens Alignment (Shift + F4)
This feature activates / deactivates the final lens alignment mode for the
fine alignment (for the electron beam only). The scanning changes to the
fastest scan value, lens modulator turns on and the alignment cross
appears in the center of all imaging quads.
Pressing activates a 5-arrow ended cursor. The mouse motion starts the
final lens alignment (see Chapter 5).
Direct Adjustments (Ctrl + F8)
opens the Direct Adjustment window (or places it over 4th Quad, if it is
already opened) for fine-tuning the beam geometry to achieve the best focus
and brightness. The controls are separated into two tabs (see Chapter 5).

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Show FIB Heat Alert

When ticked, the system informs an user 1 minute prior to the automatic
FIB Heat procedure (started when ion emission beam is lower then
approx. 2 µA) and enables to stop it (see Chapter 4: 253 - Supervisor:
Ion Beam alignment).

Patterning Menu (Alt + P)

opens the Patterning menu functions (see Chapter 5):
Start / Pause / Resume Patterning (Pause button)
starts / pauses patterning of the enabled pattern(s) in the active quad.
The menu item and a corresponding toolbar icon changes according to
actual condition.
Reset Patterning (Ctrl + Pause button)
cancels the patterning procedure.
Next Pattern (Shift + P)
In serial patterning the actual Patterning is stopped and the procedure
continues with the next pattern (if present).
Next Line (Ctrl + N)
When milling a Cleaning Cross Section pattern type, milling of an actual
line is cancelled and continues with the next one.
Previous Line (Ctrl + Shift + N)
When milling a Cleaning Cross Section pattern type, milling of an actual
line is cancelled and continues with the previous one.
Sleep After Patterning
When selected, this function applies the System module / Sleep
command when patterning process finishes.
Autostart Real Time Monitor (RTM)
When selected, this function releases the pause function for the quad
with patterns enabling automatic start of the real time monitoring of the
milling process.
Live RTM after Snapshot
After acquiring a snapshot RTM feature continues automatically.
Blackout Pattern Area for RTM
In case the Real Time Monitor is running, the area not milled is darkened
to enhance the visibility of the RTM information. The visibility of the
individual patterning pixels is greatly enhanced (this is especially important
for patterns with extremely large pitch or very thin lines).

FIGURE 3-7 IMAGING with / without BLACKOUT PATTERN AREA

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Autostart iSPI Electron Acquisition

When ticked and iSPI is on (intermittent Switching between Patterning
and Imaging) starts automaticlally when starting patterning. Electron
beam is released, when paused. When not ticked, nothing happens.

Stage Menu (Alt + S)

opens the stage and sample navigation functions:
xT Align Feature
opens the procedure that helps to navigate along a feature that extends
off the screen at the desired magnification. The procedure uses the
stage rotation (see Chapter 5).
Scan Rotation Align Feature…
opens the procedure that helps to navigate along two sample points. The
procedure uses the scan rotation (see Chapter 5).
Compucentric Rotation (F12)
places a green circle in the selected quad. By rotating the circle a
different viewing orientation of the sample area can be achieved by a
physical stage rotation and adjustment of X and Y axes. Stage rotation
keeps the observed feature in the center of the field of view. If this does
not occur, the alignment should be performed to locate the stage center
and calibrate the stage (see Chapter 5).
Define User Units…
activates a procedure guiding an user to determine User Units for X and
Y stage axes. These are used for relative stage movements associated
with the regular features mapping (in particular integrated circuit
applications) (see Chapter 5).
User Units
organises the stage software to recognise the defined user units rather
than the default metric measurements. The X and Y coordinates now
operate in User Units which are indicated in the Stage module /
Coordinates tab by the UU symbol (see Chapter 5).
Beam Shift Reset
zeroes the beam shift. A feature observed with a non-zero Beam Shift is
automatically moved back to the imaging center using the stage.
Zero Beam Shift
zeroes the beam shift without moving the stage. A feature observed
before selecting this function is moved from its position by the measure
of the applied beam shift.
Auto Beam Shift Zero
automatically resets the beam shift each time it reaches the maximal
value during the Get function (the point-to-point stage movement) and
corrects the image position with a stage movement.
Home Stage (Shift + F3)
starts procedure which moves all motorized axes to their hardware limits
and ensures that the physical stage position agrees with the coordinates
readout. During the home stage procedure the xTm: Stage Information
dialogue displays its progress. The stage axes are moved to their end-
switches in the following order:
1. Z (lowest position), 2. T (tilt), 3. X, Y and R (rotation) at the same time.
When the stage is homed correctly it ends up in the following position:

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X / Y position is set to the factory pre-set stage rotation centre, R = 0°, T

= 0°, Z = preset long working distance (depends on the stage type).
Home Stage Without Rotation
executes Home Stage function (see above) without rotation. When the
stage is homed without rotation the stage Rotation reference is greyed
out. This is useful when a large specimen is inserted and stage rotation
could cause a collision with equipment inside the chamber.
Center Position (Ctrl + 0 - digit)
moves the stage to coordinates X = 0, Y = 0.
Touch Alarm Enabled
activates the Touch Alarm for the stage. This function automatically stops
the stage movement and displays Touch Alarm warning dialogue
whenever the stage or a conductive specimen touches the objective lens
or any other equipment conductively connected to the chamber. This
functionality is used also when the stage engines start to rise the power
over the determined level.
External Current Measurement
When ticked, the Status module / Speciment current value is N/A,
because it is expected to have an external measuring device (option)
connected (see Chapter 7).
Unlink Z to FWD
This feature functions in an opposite way as the following one. 
The Z coordinate value represents then the distance from the Z home
position (stage base). The dialogue warns you about the stage Z axis
positive move direction.
Link Z to FWD (Shift + F9)
sets the Z coordinate value to the actual Free Working Distance (FWD)
value. This allows accurate movement between the sample top surface
and the end of the objective lens. The related toolbar icon changes
according to the Z-coordinate status:
• Greyed icon: the function is disabled – the high voltage is switched off
(so there could be no electron imaging) or all quads are paused.
• Red question mark: the function is enabled – Z is not linked to FWD.
Use this function as soon as possible, after a proper focus.
• Red circle: the function is enabled – Z is roughly linked to FWD, but it
needs correction. It happens e.g. after: changing the specimen, focusing
and linking Z to FWD at a long WD and then moving the stage to a short
WD. Focus carefully at a WD around 10 mm and use this function again.
• Green double-ended arrow: the function is enabled – Z is properly
linked to FWD. Now it should be safe to change the working distance
by setting a Z coordinate in the Stage module.
Enable Z-Tilt map
Some movements of the tilted stage are not safe because of a possible
collision with the final lens. The table (not user editable) with a pairs of
values indicates the maximum safe Tilt angle for a certain Z value when
coupled. It can be used to guarantee safe usage of the stage (tilt restriction)
for a flat samples only and when a proper Link Z to FWD is established.
Enable Safe Stage Moves
When ticked the software takes into account all accessories installed
inside the chamber. That’s why the stage doesn’t move to the target
position following the straight path. When the magnification is large and

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stage movements are expected to be tiny, it is not necessary to switch on

this functionality.
Tilt 0° (Ctrl + E) / Tilt 52° (Ctrl + I)
tilts the stage to 0° / 52°.
Sample Navigation (Ctrl + N)
toggles on / off function that enables to navigate electron imaging (scan
field) towards desired places on a specimen using either paused or
loaded sample image (usually captured at much lower magnification).
The Sample Navigation can be selected independently for any quad,
regardless of its actual content and status. A tick next to the menu item
indicates that the function is selected for the selected quad. As soon as
this quad is paused, the Sample Navigation indicator appears in the
upper right corner of the quad. The indicator is green as long as the
paused imaging can be used to navigate the live one, otherwise turns
read (e.g. when the stage rotation or tilt changes).
Navigation Montage...
This procedure captures the sample image to be used in the Sample
Navigation (see Chapter 5).
Navigation Alignment...
This procedure alignes the sample image according to specific demands
(see Chapter 5).
Move Stage to Nav-Cam / Take Nav-Cam Photo (Ctrl + Shift + Z) /
Restore Last Nav-Cam Photo
Helios NanoLab 450 S / Helios NanoLab 450 S / Helios NanoLab 450 ML
This items control the Nav-Cam navigation feature (see Chapter 5).

Tools Menu (Alt + T)

opens the Tools menu functions:
Image Registration
With user-specified alignment points one can transform one image
spatially to correspond to another one, then use that new one as if it
were an image of the sample. The transformed image could include one
taken with the optical microscope that corresponds to the real sample, or
several taken at various depths of focus. This is also called image-to-
image registration and image alignment.
Click the Image Registration… and follow the prompts. The user first
selects the quad with the reference image and then the quad with the
target image (this is the one that will be transformed). After this a single
or multipoint alignment can be applied by selecting similar points in both
the reference and target image. Register will apply the transformation
after 1, 2 or 3 pairs of points have been selected .
Register button will re-apply the registration on any new or restored
image in the same or a different quad. When Show is selected from the
Overlay panel a copy of the registered target image will be shown (in
red, green or blue) on the reference image which shows the quality of the
registration and to allow information from both images to be used in
placing patterns. The Threshold value (0 to 255) determines which gray
levels of the target image are shown in the overlay.
After registration the micron bar and magnification of the target image
take on the same values of the reference image. Any operation that is
applicable to an acquired SEM image can be applied to a transformed
image, including saving a file.

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Auto Contrast Brightness (F9)

ACB activates the automatic contrast and brightness routine. The system
attempts to set the Contrast and Brightness of the selected detector in
the active quad to suit the actual sample and conditions so that the
majority of grey levels is displayed.
Auto Focus (F11)
activates the automatic focus routine. The system attempts to correct 
the focus independently of the working distance or Z-coordinate set.
Note: 
When ACB / Auto Focus is activated the dialogue appears to show the
progress. The function can be interrupted by clicking the Stop Now
button, which leaves the setting at the current stage of progress. Clicking
the Cancel button before the function ends returns the setting to its
original value.
Set Default Parameters (Ctrl + D)
This functionality loads default settings. It switches UI to quad Image
mode and selects the default detector for quad 1 and the CCD camera
for quad 4. The microscope and image parameters are selected so that
there is a big chance to get usable and prompt imaging.
Display Saturation (Shift + F11)
displays signal clipping in the selected quad by means of replacing the full
black / white with dark blue / yellow color. The function can be used both
for electron and ion imaging, but cannot be applied to the optical imaging.
The saturation display is selected independently for each quad. A tick
next to the menu item indicates whether the function is active for the
selected quad.
Image Post Processing (Ctrl + F7) / 
Undo Image Post Processing (Ctrl + Shift + F7)
Starting this function corrects image properties according to the Image
Enhancement module / Process tab setting (see below).
Sample Cleaning…
This feature starts the sample cleaning procedure set in the 
101 - Plasma Cleaning alignment (see Chapter 4). This cleaning
method is effective process for removing very thin contamination layers,
which are typically formed by hydrocarbons residues remaining on
vacuum parts after conventional cleaning or could be transferred into the
microscope chamber with sample (see Chapter 5).
Lab Notes…
opens the Windows Notepad application over the UI for an user to make
immediate notes and remarks. The Lab Notes can be used to open, edit
and save any text file without the necessity to hide the xT UI.
FEI Movie Creator…
provides a dialogue over the UI for setting up a collection of sequenced
TIF images, and lining them up into an AVI movie (see Chapter 5).
Application status…
The dialogue is displayed above Quad 4 showing continuously updated
system Messages. The System status tab offers informations about the
system hardware, which are used for service engineers.
• Pop-up on Message Severity: None / Error / Warning / All 
specifies which kind of messages is going to be shown automatically
on screen. Three icons in the lower right corner enable to separately

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Software Control: xT microscope Control Software

switch on / off displaying of Error / Warning / Information messages.

• Clear button clears all actual messages from the window.
• Hide button hides Application Status window.
• Three icons in the lower left corner enable to switch on / off
displaying of errors, warnings and informational messages.

FIGURE 3-8 APPLICATION STATUS

Window Menu (Alt + W)

opens the Window menu functions:
Center Cross (Shift + F5)
places a cross in the center of all electron quads. This function is
automatically used in Alignment procedures to aid the centering of
features and can be used to align a sample against a stored image in
another quad.
Alignment Rectangle (Shift + F6)
places a dashed rectangle in the center of all electron quads. This
function is used for some Alignment procedures automatically.
CCD 4 mm Marker
places a short horizontal line with 4 mm label in all optical quads to help
user with a sample positioning to a correct working distance and with the
first focusing. Only Supervisor is allowed to change the marker position
by double-clicking a new position and by confirming this action in the
popped up dialogue.
CCD Axis Marker
places axes indicator in all optical quads to help user with 3D orientation.
Crosshair Cursor
shows the cursor as a rectangular cross through the entire quad.
Undo / Redo Digital Zoom #x
When using the digital zoom (see below), it is possible to undo / redo the
last magnification / reduction step.

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Large Image Window (Ctrl + F5)

This function activates / deactivates the full screen quad imaging on the
secondary monitor.

FIGURE 3-9 LARGE IMAGE WINDOW

Large Image Window Configuration

Here one can select, whether to show an Active quad, or any selected
one. Activating the Use Single Image Size option sets the imaging
window size corresponding to Single Image mode size. These options are
also available in the bottom right corner of the large image window.
Remote Display Mode
When using the Remote Imaging (option) this feature enables correct UI
imaging at the remote site. It is also used for a remote service.
Use of this function decelerates slightly a UI performace and it is
displayed in the bottom left quad corner.
Single / Quad-Image Mode (F5)
toggles the imaging area between two possibilities:
• Single Image mode displays one quad over the whole UI imaging
area – useful for observing details.
• Quad Image mode is useful for comparing imaging of the same
sample area taken with different beams, detectors or scan conditions.
Quad 1 / Quad 2 / Quad 3 / Quad 4
The selected quad is indicated by a tick next to the respective number. In
the quad Image mode, quad 1 / 2 / 3 / 4 is displayed top left / top right /
bottom left / bottom right. In the Single Image mode, the selected quad is
displayed.

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Software Control: xT microscope Control Software

Help Menu (Alt + H)

opens the Help menu and system informations functions:
Documentation… (F1)
The Help window shows complete User Manual in PDF format using an
embedded Acrobat Reader with its useful navigation, search and
selection tools.
Clicking the Question mark at the right side of the module header (see
below) opens the respective part of the user manual.

FIGURE 3-10 DOCUMENTATION

Keyboard Shortcuts…
The shortcuts list in tables is displayed in the same way as the on-line
documentation (see above) and with the same behaviour.
About xTUI…
displays a window with a microscope picture containing information
about the product version. The window automatically disappears after
any mouse click.

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 Software Control: xT microscope Control Software

TOOLBAR
displayed below the Menu bar is made up of functional icons linked to the
most frequently used system controls. It also contains group of icons for
quick switching between UI Pages. The toolbar can be a bit different in
content or style (see the Preferences… / General tab).

FIGURE 3-11 THE TOOLBAR

Rest the cursor over the icon for two seconds without clicking it to see its
explanatory tool-tip.
Whenever you select a function the corresponding icon is highlighted to
indicate that the function is active (except of auto-functions, which
display a progress dialogue).
Note: 
If any icon represents a menu function, refer to the corresponding menu
for its description.

Magnification / High Voltage / Beam current List Boxes

Click the list box to open a selection of the pre-set and actually allowed
values, choose one and it is applied immediately (see the
Preferences… / Presets tab).

Imaging Pixel Resolution List Box

This list contains available imaging pixel resolutions (also used for
captured images). Selecting a new resolution results in the immediate
change of the scanning raster and since the present dwell time remains
unchanged, the actual scanning frequency (both Line and Frame time)
changes.

Direct Measurement
This button enables to quickly access the measurement tool without
necessity to change a page. Clicking the icon activates (yellow color) /
deactivates (grey color) the functionality (see Chapter 5).






FIBI (FIB Immersion)

This utility enables to quickly switch from an ion imaging to an electron
UHR imaging. The icon is not accessible if following conditions are not
accomplished:
• electron HV =< 3 kV
• ion HV = 30 kV

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Software Control: xT microscope Control Software

IMAGING AREA
The xT microscope Control software (UI) uses 4 independent image
windows – quads for imaging samples. Each quad can contain imaging
from any detector (including External and CCD), paused imaging or
images loaded from a file. Additionally, quad 3 can display a mix of
imaging from quads 1 and 2, and quad 4 can display a mix of imaging
from quad 1, 2 and 3.
It can be displayed either 4 quads at the same time – Quad Image mode
or one quad over the UI imaging area – Single Image mode.
Each quad consists of its imaging area, adjustable Databar containing
the imaging parameters, selectable overlay (user-defined coloring,
annotations, measurement) and some status symbols (Pause, Sample
Navigation, etc.).
At any time, just one quad is selected (has focus), and all functions
(related to a single quad – Pause, Sample Navigation, image
processing) applies only to imaging in this quad. The selected quad is
marked by the highlighted (blue) Databar.
Depending on the quad content and the status, some mouse functions
are available over its area:
• Electron imaging (incl. External and Mix): focus, astigmatism
correction, Beam Shift, magnification change (coarse, fine), zoom (in
/ out), lens alignment, Scan / Compucentric Rotation, XY-move (get or
tracking mode)
• Ion imaging (incl. External and Mix): focus, astigmatism correction,
Beam Shift, magnification change (coarse, fine), zoom (in / out), Scan /
Compucentric Rotation, XY-move (get or tracking mode)
• Optical imaging: 4 mm Marker placement, Compucentric Rotation,
Z-move (tracking), Tilt
Note: 
Due to a hardware limitations, some detectors cannot be used
simultaneously. They can still be selected for different quads at the same
time, but if one of them is started, the other quads with incompatible
detectors are automatically paused. 
The optical imaging is automatically activated (if it is paused), when the
venting procedure starts.
Image Databar
displays optional instrument, imaging and labeling information. They can
be placed in any order and expand or contract to fit the quad width as
long as there is enough room (see the Preferences… / Databar tab).
Clicking some of the image databar fields induces an active menu
related to it with appropriate choices. Additionally clicking the label field
induces the label editing menu and double-clicking the micron bar
induces the image properties window (see above).

FIGURE 3-12 THE DATA BAR EXAMPLES

Selected electron imaging

Unselected ion imaging

Unselected optical imaging

Selected Patterning Imaging

Unselected Patterning imaging

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 Software Control: xT microscope Control Software

Note: 
The Databar information are always related to the live imaging. If the
imaging is paused or an image is loaded from a file, they could differ from
actual system conditions.

PAGES (ALT + P) AND MODULES

The software controls on the right side of the screen are organized into
Pages, which are divided into Modules holding specific functions. The
required page can be selected either by pressing the corresponding icon
button or with the use of short-cuts (see below).
TABLE 3-1 PAGES AND MODULES LIST

Pages Modules (Tabs)

Beam Control 1. Vacuum, 2. System, 3. Column, 4. Magnification, 
5. Scan Rotation, 6. Beam, 7. Beam Deceleration, 
8. Detectors, 9. Status
Navigation 10. Stage (Map / Coordinates / Tilt Correction) 
or (Bulk / Flip / Tilt Correction), 11. Stage Z, 
12. Loadlock, 8. Detectors, 9. Status (reduced)
Patterning 13. Pattern (Basic / Advanced / Progress / S Mill), 
14. Omniprobe, 15. End Point Monitor (iSPI / Monitor
/ Settings), 9. Status (reduced)
Processing 16. Measurement / Annotation, 17. Digital Zoom, 
18. Enhanced Image (LUT / Mix 3 / Mix 4 / Color /
Process ), 8. Detectors, 9. Status (reduced)
Detectors 19. Detector Settings, 20. Quad Presets, 
7. Beam Deceleration, 8. Detectors, 9. Status
Sample 13. Pattern (Basic / Advanced / Progress / S Mill), 
Preparation 14. Omniprobe, 5. Scan Rotation, 
10. Stage (reduced)
Alignments 21. Alignments (Instructions / Individual steps),
9. Status

Note: 
The number in front of the module name represents an order in which the
modules are introduced in the following text. 
For Software Interface Elements control see above.
Some of the module controls are beam dependent. In this case, an
active beam type is indicated by the corresponding icon at the right-hand
side of the module.

1. Vacuum Module
is used to control the pressure in the specimen chamber. The Pump
button starts the pumpdown procedure for the specimen chamber and
the column. The Pump with Sample Cleaning… choice pumps the
system, makes Sample Cleaning procedure (see Chapter 5) and
remains columns evacuated. The system allows the accelerating voltage
to be switched on only when the columns are sufficiently evacuated. The
Vent button starts venting for a sample exchange after the user
confirmation (see Chapter 2).

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2. System Module
contains the possibility to carry out several operation in one click:
The Wake Up Button
• starts the Ion source
• starts the Electron source (if it is switched off)
• switches the electron and ion beam accelerating voltage on
The Sleep Button
• switches the electron and ion beam accelerating voltage off
• stops the ion source
• switches the GIS’s heating off

3. Column Module
contains controls for setting the electron beam conditions:
Beam On Button
switches the accelerating voltage on / off.
Beam Current Preset Adjuster
enables to adjust the electron Beam current in the selectable accuracy
steps (see the Preferences… / General tab). The actual value from the
factory preset list is displayed in the text area of the adjuster, toolbar
(default) and in the Databar (if selected). Only values usable for actual
imaging conditions are displayed.
High Voltage Preset Adjuster
enables to adjust the overall electron acceleration voltage (from 200 V to
30 kV in 100 V steps) either continuously or using the pre-set values (see
the Preferences… / Presets tab). The actual High Voltage value is
displayed in the text area of the adjuster, toolbar and in the Databar (if
selected).

4. Magnification Module
The continuous adjuster offers a variety of ways to control the actual
imaging magnification (see above). The magnification range changes
dynamically according to the working distance and can also be controlled
with the use of other tools (see Chapter 5).
Magnification Control
The Couple Magnification check box ensures the same magnification
for electron and ion beams.
• Clicking the end arrow increases magnification by about 5%.
• Clicking between the end arrow and the button increases
magnification by about 20%.

5. Scan Rotation Module

controls and displays the Scan Rotatio value (see Chapter 5).

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6. Beam Module
Stigmator 2D Control
enables to correct an image astigmatism. The crosshair cursor indicates
the actual setting.
Shift + Right-clicking over an electron imaging quad triggers the
astigmatism correction. Unlike the 2D box control, this is magnification
sensitive and therefore it suits for fine corrections at high magnifications,
or employ the Adaptive Sensitivity functionality (see above).
Beam Shift 2D Control
indicates and controls the beam shift with respect to the objective lens
axis. It is useful for fine image shifts without stage movement.
Shift + Clicking over an electron imaging quad triggers the Beam Shift
function. The mouse cursor changes to a hand one that "holds" the
image and drags it over the screen. Because of a limited Beam Shift
range, this works well only for high magnifications, or employ the
Adaptive Sensitivity functionality (see above).
Note: 
Right-clicking over the 2D box opens the menu with following particular
choices:
• The Reset sets the Beam Shift value to zero and moves the stage to
compensate the resulting imaging shift (same as the Stage menu /
Beam Shift Reset function).

7. Beam Deceleration Module

In the Beam Deceleration mode a negative potential (Stage Bias) is
applied on the stage, which influences both primary and signal electrons.
It allows to decelerate the primary beam up to 50 V landing energy (see
Chapter 5). 

8. Detectors Module
contains continuous adjusters to control the active detector Contrast
(detector voltage) and Brightness (voltage offset). The values are
remembered for each detector and a quad. The adjusters are disabled if
the detector is not available or cannot be controlled (e.g. CCD camera or
an External detector).
Contrast & Brightness Continuous Adjusters
Regardless of the detector actual gain range, the Contrast & Brightness
range is always 0 - 100 (%) and the small / large step size is 0.1 / 1 (the
Brightness step size may differ for some detectors in order to achieve a
sufficient sensitivity). A direct value can be entered by double-clicking
the Contrast / Brightness value.

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9. Status Module
can be found at the base of most 
pages, displaying the following information in a full or any constricted
form, some of them as a tooltip (said values are approximate only):
• The Specimen Current: shows the electron current reaching the
specimen.
• The Ion Beam Current: shows the ion beam current.
• The Chamber Pressure (Chamber): shows the specimen chamber
pressure.
• The E Source / E Middle / I Source / I Bottom / Chamber: 
shows pressure in the corresponding vacuum system section.
The system conditions are displayed by means of the icons:
TABLE 3-2 STATUS ICON MEANING

Icon Status
Gun space Vacuum / Chamber Vented 

Gun space Vacuum / Chamber Pumping or Venting 

Gun space Vacuum / Chamber Vacuum 

(ready for the microscope operation)
Stage axes – Lock (any one) / Unlock (all) 

Dynamic Focus is On 

Scan Rotation is not zero 

Degauss is restricted 

External scanning mode is On 

10. Stage Module

consists of the tabbed sections varying according 
to the microscope model (see Chapter 5).
Helios NanoLab 450 / Helios NanoLab 650 / Helios NanoLab 600i
• The Map tab displays the stage positions location in a visual map
form and as a list for selection.
• The Coordinates tab displays numerical values of a particular
position. Stage movements along selected axes could be locked.
• The Tilt Correction tab contains correction features for the tilted
imaging.
Helios NanoLab 450S / Helios NanoLab 450ML
• The Bulk / Flip tab combines features of Map and Coordinates tabs.
Note: 
The stage movement can be aborted by hitting the keyboard Esc key. Don't
hesitate to do so if you are not sure that the initiated movement is safe!

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FIGURE 3-13 THE STAGE MODULE

11. Stage Z Module

This module enables to softly move the stage in the Z-axis 
direction. The more the slider is pushed to the each side, the faster is the
stage motion. Clicking the slider bar or the arows at its ends moves the
stage about an infinitesimal distance.

12. LoadLock Module

Helios NanoLab 450 S / Helios NanoLab 450 ML
The loadlock enables sample exchange to the specimen chamber,
eliminating the need to vent and evacuate the entire specimen chamber
during exchanges (see Chapter 5).
• Pressing the Clamp push button (on the LoadLock body) attaches the
carrier onto the loadlock arm.
• Clicking the Load button moves the sample on the carrier into the
chamber.
• Clicking the Unload button moves the sample out of the chamber into
the loadlock.
• Pressing the Release push button (on the LoadLock body) loosens
the carrier from the loadlock arm.
The Load with Sample Cleaning… choice pumps the system, makes
Sample Cleaning procedure (see Chapter 5) and remains columns
evacuated.

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Software Control: xT microscope Control Software

13. Pattern Module

A pattern type can be selected and handled by using the icon 
buttons on top of the module. It can be drawn in the selected quad and
then it is displayed in the pattern list with a relative number. The pattern
properties could be changed via the Basic and Advanced property
editor. The Progress indicator displays the Overall / Current Progress
(over time) of the active patterning. The S. Mill tab enables to process
only specified grey levels of the selected pattern (see Chapter 5).

FIGURE 3-14 THE PATTERN MODULE

14. Omniprobe Module

Model difference: 
Option for 
Helios NanoLab 450 / Helios NanoLab 650 / Helios NanoLab 600i.
This module operates the micro manipulator, which allows you to extract
a TEM sample in situ. By selecting / deselecting the Insert Omniprobe
checkbox the Omniprobe needle can be inserted / retracted. Movements
of the stage are possible with Get and Relative moves while the needle is
inserted. Instructions for use of the Omniprobe are supplied by the
Omniprobe Company independantly with each Omniprobe device.
The Alternate E/I check box functionality is the same as the Scan menu
\ Alternate Electron/Ion scanning item (see above).

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 Software Control: xT microscope Control Software

15. End Point Monitor Module

This set of features enables to monitor a milling process in detail,
enabling to grab inspectional images during the progress 
(see Chapter 5).

FIGURE 3-15 THE END POINT MONITOR MODULE

16. Measurement / Annotation Module

combines tools for measuring and making annotations in imaging.
A measurement tool, an annotation shape or a text label can be selected
from the first three icons on top of the module, and then drawn in an
imaging quad. All objects are sequentially indexed and displayed in the list
box below icons. The properties of the objects are possible to change in
the property editor (see Chapter 5).





17. Digital Zoom Module

The procedure takes place in the computer memory only and helps to
navigate across the enlarged view. Click the + / - magnifying glass
button to enlarge the view in the selected quad. Click the switching
button to turn over a digital magnification last used and a normal view.
Press and drag the green bordered area inside the digital zoom image or
click inside the green rectangle and move it by Ctrl + keyboard arrows to
change an observed area in the selected quad. Change the observed
area by dragging the green borders.
When the digital zoom ratio is applied, the icon appears in the
appropriate quad.

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18. Enhanced Image Module

consists of four tabbed sections offering various digital image
enhancements. In contrary to Detector module / Contrast and
Brightness functions, these enhancements are applied only to the
active quad independently. In case the user changes the default settings
of LUT / Color / Process tab, its background color changes to green.
The digital processing can be applied to any live, paused or loaded
image, including an optical one (see Chapter 5).

FIGURE 3-16 THE ENHANCED IMAGE MODULE

19. Detector settings Module

enables to choose the selected quad detector and adjust its parameters.
Detector List Box
contains list of detectors actually available for the selected quad (the
same as enabled items in the Detectors menu). The list box always
displays the detector actually selected in the selected quad.
The rest of the module dynamically changes according to the selected
detector and its parameters, which may change from quad to quad (see
Chapter 5 and 7).

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20. Quad Presets Module

The Import / Export button functionality is the same 
as the File menu / Import / Export items (see above).

21. Alignments Module

contains alignments which enable to optimize the system performance
(see Chapter 4).
• The Alignments list box contains list of Alignment procedures
available for the actual user level (User, Supervisor or Service).
• The Instructions info box displays the selected alignment procedure
instructions.
• The Steps module shows an actual alignment page with all
necessary components.
Caution! 
An user must understand the procedures at the appropriate level before
proceeding with any adjustment. Improper alignments can make the
system difficult to use.
Note: 
Some alignment modules may have some features distributed differently
than others, but functionality is almost the same, if it is not mentioned.

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Software Control: FEI User Management Software

FEI User Management Software

The FEI User management software allows to FEI Account Admistrators,

FEI Supervisors and FEI Microscope Users to organise user accounts
that can possibly be used to run the xT microscope Control software. It
allows the creation and removal of user accounts, the setting of user
passwords and group membership, as well as the copying and removal
of user data.
You can start the software from the system Start menu. This brings up
the Log On dialogue box, containing Username and Password text
fields, for entering the User Management software.

CONTROL POSSIBILITIES
• Context menu – You can reach some context options by right-
clicking (see below).
• Drag and Drop actions – Instead of using menu options, you can
sometimes simply drag and drop items from one icon to another (set
user group).

FEI ACCOUNT ADMINISTRATORS

As the highest account level, FEI Account Administrators have rights that
allow them to create and delete users and change their properties over
the following user groups (in order of significance):
• FEI Account Administrator
• FEI Supervisor Users
• FEI Microscope Users
• FEI Non-active Users
Each of these accounts has its own opportunity to operate the
xT microscope Server and Control software. The first FEI Account
Administrator is created during the system installation.

FIGURE 3-17 FEI ACCOUNT ADMINISTRATORS CONTROL OVERVIEW

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 Software Control: FEI User Management Software

File Menu
contains the following items:
• Log On: click to log on (active when user is logged out).
• Log Out: click to log off (active when user is logged on).
• Refresh (F5): click to refresh the user tree.
• Exit: click to exit the FEI User management program.

Account Menu
contains the following items, which are accessible only for FEI Account
Administrators (with the exception of set password function). 

• Create (Ins): click to add a new user or supervisor. 















• Remove (Del): click to remove an existing user. An user must be

highlighted first.
If an FEI Microscope User has user data, the account administrator is
warned that user data will be removed also. If any additional user is to be
removed, that additional user’s data is removed without warnings. 





• Set password: click to make a password for an user. An user must

first be highlighted in the tree. 
An FEI Account Administrator can change the password for any user
from a lower level account.




• Set user group: click to set the group for an user. An user must first
be highlighted in the tree. When confirmed, an user is moved to
selected group. When moving an user from the FEI Microscope Users
group to the FEI Non-active Users group, his user data will be
removed. A warning is displayed in this case.

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Software Control: FEI User Management Software

• Properties (Alt + Enter): click to see and change the properties for
that user. An user must first be highlighted in the tree. 








Userdata menu
contains the following items.
• Copy (Ctrl + C): click to copy user data from an user of the same or a
lower level group.
• Paste (Ctrl + V): click to paste user data into your own account or into
the accounts of a lower group level. It is not possible to copy user
data inside the FEI Supervisors User group.
• Remove: click to delete user data from a selected account of equal or
lower group level.

Help Menu
contains the following items: 

• Legend: clicking provides an explanation of icons used in the tree. 









• About: displays the FEI User Management software version and

copyright.

ACCOUNT LOGGING
This accounting utility monitors user, log on / off actions, session time,
filament lifetime and the UI status. It works with two log files located in
the directory c:\Program Files\FEI\data\accounting\:
• accounting.tmp is a temporary running file during use of the
equipment at each user session, updated every 15 seconds so that
any power down or operating system crash situation can be time
logged.
• accounting.log is permanent file to which the previous data are sent
when a new session is started. This file is only readable by the FEI
Supervisor User or higher level.
These files can only be deleted at factory or service level. Each one is a
text – CSV file so it can be loaded into Microsoft Excel for processing. 
It can also be viewed by the particular FEI utility:
c:\Program Files\FEI\Exe\feiaccountinglogviewer.exe

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 Software Control: Preferences… Dialogue

Preferences… Dialogue

This dialogue can be opened by selecting Preferences… 

(Ctrl + O - letter) from the pull-down menus: Scan, Beam, Patterning,
Stage and Tools. The opened menu from which it is chosen dictates the
tab opened on entry. Once the Preferences dialogue is opened, any of
the tabs can be chosen.
The Preferences dialogue consists of tabbed sections. Clicking the
required tab opens a section that allows changing and presetting
conditions for a group of the related functions. Only one tab can be
opened at any time.
The items changed remain valid (for a specific user) until changed for the
next time.
Some of the preference controls are beam dependent. In this case, an
active beam type is indicated by the corresponding icon and items
change accordingly.

Units Tab
allows an user to change the Units of Measure and Pressure. The
choices affect the Stage module input boxes, the databar display, the
status module and so on.

FIGURE 3-18 UNITS PREFERENCES

Selection possibilities are:

• Units of Measure: millimeter [mm] / micrometer [µm]
• Pressure: Pascal [Pa] / torr [Torr] / millibar [mbar]

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Software Control: Preferences… Dialogue

Movie Tab
provides two groups of controls: Timer to set-up the movie frame-rate
and File to set-up the path name and format of the resulting movie (see
Chapter 5).

Databar Tab
specifies content of the databar displayed at the base of all quads. The
configuration and available items differ for the beam selected (Electron /
Ion / Optical) for the selected quad. The Label can be set independently
for each quad.

FIGURE 3-19 DATABAR PREFERENCES

There are two lists in the dialogue, one labeled Available and the other
Selected. Items in the Available list can be added / removed individually
(> / <) or as a whole (>> / <<) to / from the Selected list. The Selected list
contains items that are displayed in the Databar. The items in the
Selected list can be Moved Up, Moved Down, Top or Bottom according
to priority or preference. This in turn changes the order of the displayed
items in the databar.
The Label and Micronbar can be chosen by ticking the appropriate
check box. Their area expands or contracts as other items are added to
or removed from the databar. The Micronbar scales to the magnification.
Clicking the Label… button brings up a dialogue to edit the label of any
quad(s). The same dialogue can be opened by double-clicking the actual
label in any quad.
Clicking the Browse Bitmap… button opens a dialogue to load a bitmap
into the databar.
Note: 
The limit for entries is displayed in the dialogue as it is updated. It is
possible to select more items than can be displayed. The databar
preview should be used to check available space.

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 Software Control: Preferences… Dialogue

Presets Tab
allows an user to change the pre-set values in the High Voltage and
Magnification drop-down lists. The configuration and available items
differ for the beam selected (Electron / Ion / Optical) for the selected
quad. A value can be changed by selecting it in the list and entering a
new one in the edit box just below the respective title. The new value
replaces the selected one and is immediately sorted into the list. The
number of entries in the list remains fixed.

FIGURE 3-20 PRESETS PREFERENCES

The High Voltage list can be changed to span any values from 200 V /
500 V to 30 kV for the electron / ion beam. The values must be entered in
kilovolts (0.2 means 200 V).
The Magnification list can be changed to hold frequently used
magnifications. Values that are in the pre-set list but cannot be applied to
the actual SEM conditions are not shown in the toolbar / Magnification
list box. Magnification range is from 20× to 1 000 000x.

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Software Control: Preferences… Dialogue

Scanning Tab
allows an user to change the dwell-times (scanning speeds) table and to
set-up the Slow scan / Fast scan / Snapshot / Photo function. The
configuration and available items differ for the beam selected (Electron /
Ion / Optical) for the selected quad.

FIGURE 3-21 SCANNING PREFERENCES

On the left side of the module there is a dwell-time preset list with the
fixed number of entries. Selected Preset values can be changed in the
Property editor on the right side of the module. The following properties
are editable (depending on the kind of the preset):
• Dwell Time: one point beam duration time
• Line Integrate: no. of line scanning repetition
• Resolution: no. of points, Width × Height (imaging resolution)
• Integrate (1, 2, 4, 8, 16, 32, 64, 128, 256): no. of integrated frames
• Acquisition: (8 bits / 16 bits) sets the captured image bit depth
• Drift Correction (Yes / No): corrects imaging drifting when averaging
filter is active. When activated, the text below the blinking quad pause
icon notifies an user.
• Continuous Scan (Yes / No): when starting up a Snapshot / Photo
function, scan in progress is finished before image grabbing starts.
This functionality is convenient for charging samples but it requires
same scanning conditions for scan in progress and Snapshot / Photo
function preset.
• Action activated at the end of Photo / Snapshot function: 
Save saves the image using an automatic file name and format,
Save As… opens the Save As dialogue to save the image,
None just pauses imaging.
• Post Processing (None / Image enhancement): enables to start
Image Post Processing after an image acquisition.

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 Software Control: Preferences… Dialogue

Following properties are informative and non-editable:

• Line Time: line scan duration time,
• Frame Time: quad scan duration time,
• Refresh Rate: imaging refresh frequency.
Slow (tortoise / large green sector) / Fast (hare / small green sector)
preset icon indicates the matching dwell-time value. To change it move
an icon up or down just by clicking-and-dragging it.
Snapshot (F4) / Photo (F2) (different cameras) preset icon indicates the
matching dwell-time value. Set all possible properties in the Property
editor.
The Default button restores the default dwell-time list and preset
settings.

Sensitivity Tab
The preset sliders control the sensitivity of the Manual User Interface
(MUI – option). The setting differ for the beam (Electron / Ion) selected
for the active quad.

FIGURE 3-22 SENSITIVITY PREFERENCES

All MUI controls are represented except the Magnification. The Default
button sets the original settings.

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Software Control: Preferences… Dialogue

General Tab
contains variety of user settings of both UI behaviour and microscope
operation, which are of less importance and/or does not logically belong
to other Preferences section.

FIGURE 3-23 GENERAL PREFERENCES

Each item of the General Preferences is represented by single line

displayed in the property editor. Clicking on the corresponding Value
displays a drop-down list with the settings available for that item.
Note: 
Some changes become visible after the next UI start.
Categories
To make navigation among the number of preferences easier, they are
divided into three groups. Selecting appropriate group from the
Category drop-down list will display in the below property editor only the
items belonging to this group. Selecting Category All will display all items
at once.
UI appearance
• Icon style (Nova / Quanta) 
Selects appearance of the toolbar icons.
• Image dimensions control (Magnification / HFW) 
Selects a way of the magnification representation and control.
• Frame active quad (Yes / No) 
Switches on / off additional highlighting of the active quad.
• Enable zooming on mouse click-and-drag (Yes / No) 
Enables / disables the function linked to the left mouse button.
• Switch sample tracking on mouse wheel click (Yes / No) 
Switches the tracking movement control linked to the mouse wheel
between click-and-move and click-and-drag modes.
• Pause stops immediately (Yes / No)
The Pause function acts instantly / waits for the complete scan.

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 Software Control: Preferences… Dialogue

• Display Scanning Preset toolbar (No / Yes) 

Enables to show 6 scanning preset parameters at the toolbar.
• Display Pattern Preset toolbar (No / Yes) 
Enables to show 6 pattern preset buttons at the toolbar.
Image and graphics
• Restart Average Filter when magnification changes (*)
• Restart Average Filter when scan rotation changes (*)
• Restart Average Filter when beam shift changes (*)
• Restart Average Filter when stage moves (*)
* – (No / Yes)
These items enable to choose whether the imaging averaging should
be restarted when the indicated parameter changes. Restarting the
average filter causes the imaging to blink and get noisier; on the other
hand, the averaging slows down the imaging response to the
changed parameter.
• Display beam icon in databar (Yes / No) 
Adds an active beam icon to the first data bar position.
• Blinking pause icon during image integration (Yes / No) 
If Yes is selected, the blinking Pause symbol is displayed in quads
which are being stopped. Otherwise, the Pause symbol appears only
after the image acquisition has actually stopped.
• Display Recording Movie message 
(No / 1 second / 2 seconds / 5 seconds / 30 seconds) 
At the beginning of the movie recording, this message could be
displayed in the recorded quads for a selected time period.
• Hide Rotation controls when not used 
(No / 10 seconds / 30 seconds / 60 seconds) 
Specifies if and when the on-image Scan / Compucentric Rotation
control should be automatically switched off.
• Display Scan Rotation in CCD quads (Yes / No)
• Display Tilt Corrections in CCD quads (Yes / No) 
The above two items specify if the Scan Rotation / Dynamic Focus
and Tilt Correction indicator and value should be permanently
displayed in the CCD image(s); only non-zero values are displayed.
• Display Stage Map in Navigation quads (Yes / No) 
shows saved positions in any navigation image, which is available
(Nav-Cam, Navigation Montage, Image Registration, Navigation
Alignment).
• Save digitally zoomed image as (Entire image / Zoomed area) 
When saving a digitally zoomed image, this option enables to save
the zoomed area or the entire scanned area.
• Show legacy scanning resolution (Yes / No) 
enables to display old format screen resolutions in the toolbar drop-
down list (see Chapter 3).
• Post Proccessing (Standard / None / Custom...) 
Sets the default Post Processing setting.
Microscope operation
• Interactive Databar (On / Off) 
Turns image databar fields to be active (when possible) / inactive.
• Scan Rotation Sensitivity (0.1 /0.01) 
Choose the Scan Rotation setting sensitivity.
• Lower stage when venting the chamber (Yes / No) 
Specifies if the stage should automatically go to a low Z values when
venting the chamber. This is a recommended (not default) setting,

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Software Control: Preferences… Dialogue

because it greatly diminishes the chance of hitting the pole piece when
closing the chamber doors after mounting a higher specimen.
• Change magnification when pumping 
(No / Set to 100× / Set to 200x) 
Specifies whether the magnification for electron imaging should be
automatically set to a low value when the chamber is being pumped
(presumably after replacing the specimen).
• Switch off CCD automatically 
(No / 1 minute / 10 minutes / 30 minutes / 1 hour / 2 hours / 6 hours) 
Specifies if and when the CCD camera and infrared LED’s should be
automatically switched off. The countdown starts when resuming the
optical quad and continues regardless of the operator activity.
• Pause beam quads when switching off HV (Yes / No) 
Specifies if the electron imaging should be automatically paused
when switching the High Voltage off.
• Continuous reduced area scanning in iSPI mode (Yes / No)
If yes is selected and the reduced area and iSPI mode is on,
Snapshot or Photo function scanning must be stoped by an user
instead of automatic stop after the pre-defined number of scans.
• Allow Beam Shift in Get mode (Yes / No) 
Enables / disables automatic using of Beam Shift when an user
requires very small point-to-point movements (double-click the
sample point at high magnifications).
• Blank E-beam / I-beam during long stage moves (Yes / No) 
Specifies if the electron beam should be automatically blanked during
long software controlled stage movements. This may protect
extremely sensitive samples from exposure to the beam in undesired
areas.
• Reverse Joystick movement (Yes / No) 
Normally the joystick movement direction corresponds to the stage
movement, so the imaging moves in the different direction. This
setting changes the stage response to the joystick movement
direction.
• Auto switch stage measurement system (Yes / No)
Automatically switch the stage measurement systems off when not
used to avoid light interference with 3rd party equipments (EDS
detectors etc.).
• Optimized collection efficiency (Yes / No) 
If yes, the inactive (paused) SE detector is prevent from taking the SE
signal to the active one. This is not recommended to use while
patterning, which can cause image quality decrease in SPI and iSPI
mode.
• Venting valve opening time (value) 
prolongs the venting time (default value is 300 sec) to eliminate
residual vacuum which makes impossible to open the chamber door
or shortens the venting time.
• Automatic Nav-Cam photo after sample loaded (Yes / No) 
When Loadlock is installed and setting is Yes, the Nav-Cam
navigation image is automatically acquired after sample loading.
• Move to zero tilt for Nav-Cam photo (Yes / No) 
Sets the stage tilt to 0° automatically when grabing the Nav-Cam
navigation photo. The stage stays at 0° tilt when finished.
• Default quad for Nav-Cam image (Quad 1 / Quad 2 / Quad 3 / 
Quad 4 / Active) this option sets the default Nav-Cam imaging quad.
• ICE saturation suppression (On / Off) 
Areas not patterned are displayed in selected color.

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 Software Control: Preferences… Dialogue

Magnification Tab
controls the imaging and stored / printed image databar magnification
display. The constant imaging pixel size is set at the toolbar. When
storing / printing an image (while in a Single or Quad imaging mode) the
databar magnification display may not be correct.

FIGURE 3-24 MAGNIFICATION PREFERENCES

The Screen preferences area sets the imaging databar magnification

display behaviour while the File / Print preferences area sets the
storage / printing databar magnification display behaviour. Selecting the
radio button activates its functionality:
• The Real screen size: the imaging pixel width is handled.
– The Active view: the databar magnification value depends on
whether the Single or Quad UI imaging mode is selected. It is
displayed in the databar and stored / printed with an image with an
icon representing the Single / Quad UI imaging mode.
– The Single image: Single image mode magnification value is
displayed in the databar and stored / printed with an image.
– The 4-quad image: Quad image mode magnification value is
displayed in the databar and stored / printed with an image.
• The Polaroid 5” film width is handled. A recalculated magnification
value is displayed in the databar and stored / printed with an image.
• The User device width (set by an user via the edit box) is handled.
A recalculated magnification value is displayed in the databar and
stored / printed with an image.
The Keep Screen and File / Print settings synchronized check box
keeps both settings identical.

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Software Control: Entering Commands in Summary

Entering Commands in Summary

USING MOUSE

Keyboard + Mouse button Function

(Shift +) Click single-arrow cursor
Control Areas: makes a selection of a control
element.
On Screen: (multiple) selection of elements
Click & drag On Screen: drag a selected area to zoom in – to fill
an imaging area with the selection (selectable in
Preferences).
Doubleclick Electron imaging: moves the selected point to the
middle of the quad.
Optical imaging: 4 mm marker placement.
Click & drag + Shift On Screen: drag a selected area to zoom out – to fill
an imaging area with the selection.
Shift + Click Pauses / Activates all quads when clicking the
toolbar pause icon.
Shift + Click & drag hand-cursor
Activates Beam Shift.
Right-click & drag double-arrow cursor
To focus drag the mouse to the left or right.
Shift + Right-click & drag four-arrow cursor
To correct imaging astigmatism, drag the mouse 
to the left / right (X stigmator) 
or up / down (Y stigmator).
Ctrl + Click & drag Activates Detectors Contrast (left-right move) /
Brightness (up-down move) control.
Ctrl + Right-click & drag four-arrow cursor with circles
Activates the Lens Alignment.
Shift + Wheel-scroll  Fine Control: increases / decreases 
Up / Down the magnification.
Ctrl + Wheel-scroll  Coarse Control: increases / decreases 
Up / Down the magnification.
(Ctrl+) Wheel-click & drag Electron / Ion imaging: activates the Track mode
for joystick-like movement over the sample surface.
Optical imaging: activates the live stage Z - up /
down move (stage Tilt - left / right move).

Note: 
The given sequence of the key press and mouse button click is important for some
functions.

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 Software Control: Entering Commands in Summary

USING KEYBOARD
TABLE 3-3 WINDOWS SYSTEM KEYS 

Key (+ Key) Function

Enter Equivalent to OK in a dialogue box.
Esc 1. Equivalent to the Cancel button.
2. Cancels the press and drag function.
3. Stops the stage motion at that point. 
Note: 
During some procedures (Home Stage for instance) use the
software Cancel or Stop button!
Tab Step key to highlight items in a dialogue box.
(Shift +) Arrows 1. Use to select between items in a group when in a list box.
2. When quad is active and selected, the stage moves
approximately (40%) 80% of the field of view in any direction
by clicking the appropriate keyboard Arrow key.
Alt (or F10) Activates menu of the active application. Hitting the underlined
character in the menu bar pulls-down the corresponding
menu.
Alt + Tab Use to switch between running applications. This starts from
the last used one, continue to press the TAB key (while holding
down the ALT key) and applications are shown one by one.
Releasing the ALT key at any time makes application just
listed active.
Alt + F4 Exits active application or Windows operating system.
Del(ete) Deletes selected text or items.
Ctrl + A Select all items
Ctrl + C  Copy to clipboard
(Ctrl + Insert)
Ctrl + V  Paste from clipboard
(Shift + Insert)
Ctrl + X  Cut to clipboard
(Ctrl + Delete)

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Software Control: Entering Commands in Summary

TABLE 3-4 FUNCTION BUTTONS AND SPECIFIC SHORT-CUTS 

Key (+ Key) Function

F1 Displays documentation
Shift + F1 Opens Image Properties window
(Shift +) F2 Starts Photo (from all quads at once)
Ctrl + (Shift +) F2 Starts / Stops Active Preset Snapshot (from all quads at once)
(Ctrl +) F3 Toggles Videoscope (in all quads) On / Off
Shift + F3 Starts Home Stage procedure
F4 Starts / Stops Electron imaging Snapshot
(Shift +) Ctrl + F4 Starts / Stops Ion imaging Snapshot (in all quads)
Shift + F4 Starts Lens Alignment procedure
F5 Toggles Single / Quad Image mode
Ctrl + F5 Toggles Large Image Window mode
Shift + F5 Toggles Center Cross display
F6 Pauses / Activates scanning
Shift + F6 Toggles Alignment rectangle display
F7 Toggles Reduced Area / Full Frame Mode
Ctrl + (Shift +) F7 Starts / Undoes Image Post Processing
Ctrl + F8 Calls up Direct Adjustment window with 
Beam / Stigmator Centering / UC tabs
F9 Starts Auto Contrast and Brightness procedure
Shift + F9 Link Z to FWD
F11 Starts Auto Focus procedure
Shift + F11 Toggles Display Saturation function
(Shift +) F12 Toggles Compucentric (Scan) Rotation tool
Ctrl + 0 - number Center Position (moves stage to X=0, Y=0)
Ctrl + B Toggles Beam Blank function
Ctrl + D Set Default Parameters
Ctrl + E Tilt stage to 0°
Ctrl + F Sets beam focus to WD = 4 mm
Ctrl + I Tilt stage to 52°
Ctrl + K Sets Spot scanning conditions
Ctrl + M Sets Full Frame scanning conditions
Ctrl + Shift + M Starts movie recording dialogue
Ctrl + N Toggles Sample Navigation
(Ctrl +) Shift + N Starts to mill (previous) next pattern line
Ctrl + O - letter Opens Preferences dialogue
Ctrl + P Opens Print dialogue

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 Software Control: Entering Commands in Summary

TABLE 3-4 FUNCTION BUTTONS AND SPECIFIC SHORT-CUTS 

Key (+ Key) Function

Shift + P Next pattern
Ctrl + R Restarts scan
Ctrl + (Shift +) S Save image(s) (from all quads)
Ctrl + T Toggless ion and electron beams imaging
Ctrl + Z Moves stage to the Last position
Ctrl + Shift + Z Starts Take Nav-Cam Photo procedure
Pause key Starts / Stops patterning
Ctrl + Pause key Reset patterning
Ctrl + (Shift +) , Set one step slower (preset slow) scanning
Ctrl + (Shift +) . Set one step faster (preset fast) scanning
Ctrl + (Shift+) Tab (Backward) steps between quads
Ctrl + Page Up / Down Left / Right steps between pages
Ctrl + 1 / 2 / 3 …  Selection of the particular page (the number corresponds to
- letter keypad the toolbar page icon sequence)
+/- Increases / Decreases the magnification 2×
* Rounds off the magnification / HFW to the nearest round value
Ctrl + +/- Scales up / down the imaging 2× (Digital Zoom)
Ctrl (+ Alt) + arrow Moves the digital zoom area (the pattern) 
by one screen pixel in the respective direction

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Software Control: Entering Commands in Summary

3-50 FEI Limited Rights Data CONFIDENTIAL

 4 ALIGNMENTS

At the Alignments page select an alignment procedure available from

the list box. Always follow the instructions given in the Instructions
module. The Step displays the present control step number and the total
number of steps. You can find some additional explanation in this
chapter.

COMMON RULES
Alignments should be performed in the quad 1. In other case it is not
possible to ensure the correct functionality of the Contrast, Brightness
and Auto functions used at the Alignments pages.
Before one aligns the Electron column, be sure that the final lens
aperture is clean and properly centred.
During adjustment procedures it is allowed to change the magnification,
the scanning speed, to use reduced area and to optimize image contrast
/ brightness. It is also possible to correct astigmatism and to focus an
image (for a particular alignment this is forbidden).
During adjustment procedures it is not allowed to change a Spot size and
a High Voltage. Do not use the Beam Shift at any time during the
adjustment procedures, as this is set to the zero value at each alignment
section. All specimen movements can be made using the stage where
appropriate.

BUTTONS AND CONTROL ELEMENTS

The following particular buttons and control elements (see Chapter 3)
have the same behaviours for all alignment procedures, when available:
• The Start button starts the procedure and proceeds with following
dialogues.
• The End button moves an user to the last step (by clicking the Next
button) to be able to finish the alignment procedure.
• The Contrast / Brightness adjusters enable to optimize the image
quality during alignment.
• The Auto button executes the appropriate alignment action
automatically for a particular voltage / spot / direction (whatever
suitable) with the use of the Image Recognition software. If this utility
does not recognize image features well, the procedure is aborted and
Warning message appears onscreen. In this case change the
imaging conditions (better focus, slower scanning, or lower
magnification) and try again.
• The Crossover button activates the Crossover mode, where the
onscreen image shows the electron source tip instead of the sample.
5 - Emitter Startup

CONFIDENTIAL FEI Limited Rights Data 4-1

Alignments:

ALIGNMENT LIST
The list of alignments accessible for a Supervisor is represented, 
the User alignments list is reduced and is represented by (U) sign.
• 5 - Emitter Startup
Enables IGP’s and electron gun - Emitter switching On / Off.
• 17 - Quick Stage Rotation Centre Alignments (U)
Sets the stage rotation center for the correct functionality of the
compucentric rotation feature.
• 18 - Accurate Stage Rotation Centre Alignments (U)
Sets exact stage rotation centre necessary for compucentric rotation
function
• 65 - UHR-FIB wait time configuration
Sets an immersion lens stabilisation time.
• 100 - Vacuum: Start IGP’s
Enables all IGP’s (electron and ion column) switching On / Off.
• 102 - Vacuum: User Tools (U)
Offers special vacuum actions not available from the UI
• 104 - Plasma Cleaning
Enables the chamber plasma cleaning and sets time of specimen
plasma cleaning
• 105 - Pre-vacuum pump operation mode
Enables to start / stop buffer cycle in order to control prevacuum
pump operation
• 114 - Gas Flush Mode (U)
This procedure is necessary when external plasma cleaner is used.
• 210 - ION: Beam Alignment
Sets the ion source parameters.
• 211 - FIB-I Ion Column Alignment
Brings SEM lens to Immersion mode.
• 253 - Supervisor: Ion Beam
Ion beam service page
• 254 - Supervisor: GIS
Resets the GIS crucible filling lifetime counter after its exchange. 
Sets the GIS heating temperature.
• E-column: UC User Alignments (U)
Set of User level electron beam adjustment procedures
• E-column: Aperture Map Selection
Enables to set a second set of final lens apertures in case the image
quality deteriorates when using the first one (one or more actually
used apertures are worn out).
• E-column: Magnification Correction (U)
User magnification calibration (see Beam menu item).
• E-column: AutoUModeSourceCentering
Automatic alignment centers the beam through U-mode aperture.
• E-column: UC Supervisor alignments
Set of Supervisor level electron beam adjustment procedures
• E-column: U-Mode aperture selection
Enables to set one of three U-Mode defining apertures in case the
imaging quality is poor.
• Vacuum Actions (U)
Set of utilities for vacuum control.

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 Alignments:

Model difference:
Helios NanoLab 600i has individual alignment list and some of the
procedures are different.

CONFIDENTIAL FEI Limited Rights Data 4-3

Alignments: 5 - Emitter Startup

5 - Emitter Startup

This procedure enables IGP’s (Ion Getter Pumps) and electron source
switching On / Off in cases of emergency shut down or the microscope
mains switch off.
Note: 
If the Emitter On button is disabled and the IGP´s are running, restart the
xT Microscope Server and try again.

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 Alignments: 17 - Quick Stage Rotation Center Alignment

17 - Quick Stage Rotation Center Alignment

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Alignments: 17 - Quick Stage Rotation Center Alignment

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 Alignments: 18 - Accurate Stage Rotation Center Alignment

18 - Accurate Stage Rotation Center Alignment

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Alignments: 65 - UHR-FIB wait time configuration

65 - UHR-FIB wait time configuration

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 Alignments: 100 - Vacuum: Start IGP’s

100 - Vacuum: Start IGP’s

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Alignments: 102 - Vacuum: User Tools

102 - Vacuum: User Tools

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 Alignments: 104 - Plasma Cleaning Alignment

104 - Plasma Cleaning Alignment

When repeated Sample Cleaning… procedure is not effective (see

above), click the Start Chamber Cleaning button, (the procedure
Duration is much longer).
Warning! 
Do not use Chamber cleaning when EDS / WDS / EBSD system is
mounted! If you need to clean system with EDS detector mounted, use
1 mm collimator and do not exceed 30 minutes once a week at most. 
Do not leave sensitive samples (including Au-C resolution test samples)
in the chamber during Chamber Cleaning (it may be damaged).

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Alignments: 105 - Pre-vacuum Pump Operation

105 - Pre-vacuum Pump Operation

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 Alignments: 114 - Gas Flush Mode

114 - Gas Flush Mode

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Alignments: 210 - ION: Beam Alignment

210 - ION: Beam Alignment

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 Alignments: 211 - FIB-I Ion Column Alignment

211 - FIB-I Ion Column Alignment

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Alignments: 211 - FIB-I Ion Column Alignment

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 Alignments: 253 - Supervisor: Ion Beam

253 - Supervisor: Ion Beam

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Alignments: 254 - Supervisor: GIS

254 - Supervisor: GIS

The time under the GIS name displays operation periods (valve opened)
for an actual GIS. Click the Lifetime reset / GIS 1 / GIS 2 / GIS 3 …
button to reset a corresponding GIS time display.
Change target crucible temperature for a particular GIS by the T slider.
Note: 
The Working Temperature unit varies according to Preferences… /
Units setting (see Chapter 3), but the Actual Temp. unit is always °C.

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 Alignments: E-Column: / Vacuum Actions

E-Column: / Vacuum Actions

Alignments not numbered run in a different environment, they are

actually the set of alignments. Most of the procedures could run
automatically by checking the Automatic check box placed next the red
star. During the procedure informational windows could be turned on / off
by the Show / Hide Window button. Cancel the alignment sequence or
continue by the Next button.
Caution! 
Read carefully the instructions provided by the system before proceeding
with any alignment!
If you have selected any e-beam alignment procedure and you want to
select any other one, you must Finish or Cancel an actualy opened
procedure first. To start alignment procedure or to stop one in progress
right-click over the red star and select required action (Start / Stop).
A confirmation dialogue is displayed.
By clicking the Cancel button, by selecting the Stop item in the menu
(see above) or by Closing the UI nothing is saved (see Restore old
results below). In all cases the alignment windows over the quads
disappear and the Stop Execution dialog appears.

FIGURE 4-1 STOP EXECUTION DIALOG

The last page of every alignment offers one or more of the following
possibilities:
• Restore old values and finish: undoes the adjustments, nothing will
be saved.
• Save new results and finish: keeps new adjustment values and
saves them. Also creates a new Restore Point.

FIGURE 4-2 LAST PAGE CHOICES

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Alignments: E-Column: / Vacuum Actions

RESULTS
The result of every step is shown by means of an icon in the result list
when performing alignment steps.

FIGURE 4-3 ALIGNMENT RESULTS

Unavailable: 
The result has never been obtained, at least not by this 
procedure. This may mean that it has never run, or that it failed to do
anything meaningful (the difference between these two is not
important).
Reliable: 
The result is trusted by the automatic procedure 
OR 
the user has passed the alignment step manually (i.e. we trust that
the user actually performed the alignment step).
Unreliable: 
The automatic procedure has done meaningful work, 
but could not decide whether the obtained result can be trusted. This
suggests to review the result manually.
Out of range: 
the automatic procedure trusts that the optimal outcome 
is outside the range of the variable to be aligned. A value is set that is
near the border of the range.
Note: 
User alignments change settings for the time of operation and do not
affect permanently the higher level alignments (supervisor).

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 Alignments: E-Column: UC User Alignments

E-Column: UC User Alignments

• N / U Mode Source Tilt

This alignment will set up the Source Tilt values to get the beam
through the EBA (Electron Beam Limiting Aperature) for different HV
and UI probe values, and the source Shift values to direct the beam
through the center of the HR lens.
• U Mode Source Centering
This automatic alignment centers the UC beam through U-mode slits.

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Alignments: E-Column: User Alignments

E-Column: User Alignments

Helios NanoLab 600i

Centers the electron source tilt and shift.

FIGURE 4-4 SOURCE TILT AND SHIFT DIALOGUE

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 Alignments: E-Column: Aperture Map Selection

E-Column: Aperture Map Selection

Try to change the aperture map when imaging is poor or the astigmatism
is not possible to correct.

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Alignments: E-Column: Magnification Correction

E-Column: Magnification Correction

This utility is intended to enhance factory calibration acuracy under

particular, user selectable conditions.
Note: 
Switch the Beam menu / Magnification Correction item on only for
calibrated conditions, otherwise it could worsen magnification accuracy.

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 Alignments: E-column: Auto UMode Source Centering

E-column: Auto UMode Source Centering

This automatic alignment centers the UC beam through U-mode

aperture.
Note: 
This alignment needs to be done every 2 days.

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Alignments: E-Column: UC Supervisor Alignments

E-Column: UC Supervisor Alignments

• Alignment Range Editor

• Auto Couple Z to WD
• Source Tilt and Shift N-Mode / U-Mode
This alignment will set up the Source Tilt values to get the beam
through the EBA (Electron Beam Limiting Aperature) for different HV
and UI probe values, and the source Shift values to direct the beam
through the center of the HR lens.
• U-Mode Source Centering
This automatic alignment centers the UC beam through U-mode slits.
• Stigmator HR
This adjustment will set up the table values for different HV of the
Stigmator balance and astigmatism correction in HR mode.
• Lens Alignment and Stigmator UHR
This adjustment will set up the table values for different HV on the
Lens Alignment, Stigmator balance and astigmatism correction in
UHR mode. Eliminates image shift during focusing and/or normal
astigmatism correction in UHR mode.
• Switch E Beam Off

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 Alignments: E-Column: Supervisor Alignments

E-Column: Supervisor Alignments

Helios NanoLab 600i

• Alignment Range Editor

• Auto Couple Z to WD
• Source Tilt and Shift
This alignment will set up the Source Tilt values to get the beam
through the EBA (Electron Beam Limiting Aperature) for different HV
and UI probe values, and the source Shift values to direct the beam
through the center of the HR lens.
• Stigmator HR
This adjustment will set up the table values for different HV of the
Stigmator balance and astigmatism correction in HR mode.
• Lens Alignment and Stigmator UHR
This adjustment will set up the table values for different HV on the
Lens Alignment, Stigmator balance and astigmatism correction in
UHR mode. Eliminates image shift during focusing and/or normal
astigmatism correction in UHR mode.
• Switch E Beam Off

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Alignments: E-column: U-mode Aperture Selection

E-column: U-mode Aperture Selection

Try to change the aperture when imaging is poor.

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 Alignments: Vacuum Actions

Vacuum Actions

• Start / Stop IGP’s

• Pump / Vent Action
• Plasma Cleaning

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Alignments: Vacuum Actions

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5 OPERATING PROCEDURES

This chapter describes how to use the Microscope system from an

application point of view. The following subjects are covered:
• Specimen Preparation and Handling
• Imaging Optimising
• Detector types and usage
• Capturing and Handling a Single Image
• Recording Movies (Saving Multiple Images)
• Stage Control
• Nav-Cam
• Loadlock
• Multiloader
• Measurement and Annotation Functions
• Patterning
• X-ray Analysis
• Plasma Cleaner

Caution! 
These procedures assume you are familiar with the xT microscope
server and xT microscope Control software (see Chapter 3), which are
necessary to start and operate the microscope.

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Operating Procedures: Specimen Preparation and Handling

Specimen Preparation and Handling

The specimen material for high vacuum must be able to withstand a low
pressure environment (without outgassing) and the bombardment by
electrons or ions. It must be clean and conductive. Oil and dust may
contaminate the chamber environment, which could hinder or even
prevent evacuation to the level needed for standard SEM nad FIB
operation.
Note: 
Always wear lint- / powder-free clean room gloves when reaching into
the specimen chamber to minimise oils, dust, or other contaminants left
inside the chamber.

NEEDED ITEMS
• Class 100 clean-room gloves
• Specimen stubs and conductive adhesive material
• Tools: tweezers, 1.5 mm hex wrench
• Prepared or natural specimen

COATED SPECIMEN
If the specimen is nonconductive (plastic, fibre, polymer or other
substance with an electrical resistance greater than 1010 ohms) the
specimen can be coated with a thin conductive layer. This conductive
layer reduces beam stir due to sample charging and improves imaging
quality.
For successful imaging, rough surfaced specimens must be evenly
coated from every direction. Biological, cloth and powder specimens may
require carbon or other conductive painting on portions of the specimen
that are hard to coat.
Coating reduces beam penetration and makes the imaging sharper. It
may mask elements of interest for X-ray analysis (thus the use of carbon
for geological and biological specimens).
For more information on specific preparation techniques, see Scanning
Electron Microscopy and X-Ray Microanalysis, 2nd ed. by Joseph
Goldstein et al., Plenum Press, New York, 1992.

MOUNTING SPECIMEN ON HOLDER

Wafers and PGA devices have individual sample-mounting procedures.
If you are using a wafer piece or other sample, attach the specimen to
the specimen holder using any suitable SEM 
vacuum-quality adhesive, preferably carbon or silver paint. The
specimen must be electrically grounded to the sample holder to minimize
specimen charging. If you are using another way to mount a specimen,
make sure the specimen is conductively attached to the holder.
Note: 
The sample holder is not directly grounded to the chamber ground
because it is connected to the BNC feed allowing to measure the
specimen current.
Inserting / Exchanging Specimen is possible with LoadLock also for
some microscope models (see below).

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 Operating Procedures: Microscope Control

Caution! 
Store samples and sample holders in a dry and dust free environment.
Dust on samples can get drawn into the electron column, degrading
imaging and requiring an FEI Customer Service.

Microscope Control

OPERATION PRE-CHECK
To ensure correct operation check the following list before continuing.
After obtaining a preliminary imaging, you can then experiment with your
own settings.

TABLE 5-1 SETUP CONDITIONS

Adjustment Electron beam setting Ion beam setting

Accelerating Select voltage relative to specimen type:  30 kV for imaging, milling,
Voltage - low kV for surface imaging, beam-sensitive depositing
samples and slightly charging samples  5 kV for cleaning
- high voltage for conductors, high resolution, 5–10 kV for large field of view
compositional info (BSE, X-ray)
For example: 
- biological sample HV = (1–10) kV 
- metal sample HV = (10–30) kV

Beam Current 100 pA at 30 kV 100 pA at 30 kV

Scan rate Fast scan (dwell time 0.1 - 0.3 µs) Fast scan

Working Set the highest specimen point  Set the stage into the eucentric
Distance to approximately 4 mm, tilt to 0°.  position and tilt to 52º.
(FWD) (yellow mark in an optical beam quad) and press
Ctrl + F (set FWD to 4 mm function).

Eucentric 4 mm 16.5 mm
Height

Magnification Set to lowest – from 50× to 200× Set to lowest – from 50× to 200×

Standard  ETD (SE) / ICE (SE) ETD (SE) / ICE (SE)

Detector

Filtering Live Live

Contrast  With contrast at minimum value adjust See Electron beam setting
and brightness to just show a change in intensity to
Brightness the screen. Increase the contrast to produce a
reasonable imaging. Increasing brightness and
decreasing contrast produce softer imaging and
vice versa.

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Operating Procedures: Microscope Control

OBTAINING IMAGING ON SCREEN

The following assumes that the electron emission is on.
1. Select an appropriate detector (see below) and resume the chosen
quad.
2. Click the Column module / Beam On button to ramp up the
accelerating voltage. An image appears in the active quad.
3. Focus the image and Link Z to FWD (see Chapter 3).
4. Adjust to a suitable magnification, optimize the image with Contrast
and Brightness, focus, Stigmator.
5. Adjust to a suitable magnification, optimize the image with Contrast
and Brightness, focus, Stigmator (see below).

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 Operating Procedures: Imaging Optimising

Imaging Optimising

PRINCIPLES OF SEM IMAGING

All scanning beam microscopes screen with the same fundamental
technique. The primary beam is scanned across the specimen surface in
a regular pattern called a raster. Normally, this raster consists of a series
of lines in the horizontal (X) axis, shifted slightly from one another in the
vertical (Y) axis. The lines are made up of many dwell points and the
time of each dwell point can be shortened or prolonged (dwell time). The
number of points per line can be increased or decreased as well as the
number of effective lines (resolution). The result is a picture point (pixel)
array. Low or high resolution imaging can be obtained by changing these
factors. The larger the pixel array, the higher the imaging resolution. The
imaging is created pixel-by-pixel in the computer memory and displayed
on a monitor screen.
The signal emitted by the specimen surface as it is illuminated with the
primary beam is collected by the detector, amplified and used to adjust
the intensity of the corresponding pixel. Because of this direct
correspondence, the pixels displayed on the monitor are directly related
to the specimen surface properties.
The raster consists of many (typically one million) individual locations
(pixels) that the beam visits. As the beam is scanned, the signal emitted
by the sample at each beam position is measured and stored in the
appropriate digital memory location. At any time after the beam scan, the
computer can access the data and process it to change its properties, or
use it to generate a display.

MAGNIFICATION
Magnification is calculated as the displayed dimension (L) divided by
the sample scanned dimension (l).
If the observed sample point size is made smaller while the monitor size
remains constant, the magnification increases. At low magnification, you
get a large field of view. At high magnification, you point only a tiny
sample area.
It is possible to set a corresponding data bar magnification readout in the
Quad Image and Single Image modes and in the saved image (see the
Preferences… / Magnification tab).

FIGURE 5-1 MONITOR IMAGING AND SCANNED SAMPLE

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Operating Procedures: Imaging Optimising

Changing Magnification
• The Toolbar list box is used to select from a predefined values.
• The Keyboard control (+ / - / *): the numeric pad plus key (+) / the
minus key (-) increases / decreases the magnification 2× and rounds
the value. The star (*) key rounds the magnification value 
(e.g. 10 063× becomes 10 000×).
• The Mouse wheel control: Coarse / fine control can be operated by
the Ctrl / Shift key and moving the mouse wheel up / down to increase
/ decrease the magnification.
• The Selected Area Zooming In / Out is a quick way of zooming in /
out on an area of interest. Press into the imaging area and drag to
make a dotted box over the area of interest (the cursor changes to a
magnifying glass with a + sign). Release the mouse and the selected
area increases to fill the whole quad (window) with respect to the
sides ratio. Shift + pressing consecutively reverses the above
described technique (the cursor changes to a magnifying glass with a
- sign). The escape button cancels the operation at any time.
• The Magnification module (see Chapter 3)
• The Digital Zoom module (see Chapter 3)

SCAN SPEED AND FILTERING

To make a good imaging it is necessary to find a balance between scan
speed, charge, sample damage and signal to noise ratio.
A noisy imaging can be improved by decreasing the scan speed. If
charge or sample damage are the limiting factors it is better to use a
faster scan speed in combination with an Average or Integrate filter (see
Chapter 3).

CONTRAST AND BRIGHTNESS

The contrast and brightness can be set manually either by adjusting the
Detectors module controls (see Chapter 3) or using the MUI (option):
1. Select a medium speed scan in an selected quad.
2. Reduce the contrast to zero and adjust the brightness to a level so
that the last gray level can be seen, by eye, before the screen goes
black.
3. Increase the contrast so that the sample imaging appears.
4. If necessary, adjust the brightness level to improve the imaging.

Using Videoscope (F3)

This mode could facilitate contrast and brightness optimization to obtain
full greyscale imaging level range.
Three yellow horizontal lines (placed over the quad) indicate white (top
line), grey (middle line) and black (bottom line) levels. The oscillogram
signal amplitude / central position reflects a contrast / brightness of the
just scanned line. If the oscillogram is cut by the bottom / top line, the
signal level is clipped in black / white. This should be avoided because
the imaging details are lost in the clipped areas.
Tuning the oscillogram exactly between the top and bottom lines for a
feature of interest (with the use of the reduced area) results in the full
detailed imaging. The signal clipping may be used to obtain harder
contrast conditions when more black and white is needed. The signal
amplitude lowering decreases the contrast, i.e. the imaging looks softer.

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 Operating Procedures: Imaging Optimising

1. Select a slow scan in an selected quad.

2. Activate the Videoscope (F3 / Scan menu).
3. Reduce the contrast to zero and adjust the brightness level to the
lower dashed line (black).
4. Increase the contrast so that the signal level just clips the upper
dashed line (white).
5. If necessary, adjust the brightness level once more so that the
average signal level is roughly in the middle.
6. The high and low peaks should just touches the dashed lines.
Note: 
Use also the following functions to optimize 
the Contrast / Brightness (see Chapter 3): Auto Contrast Brightness (F9),
User Auto Contrast Brightness, Display Saturation (Shift + F11).

FOCUSING
Find a feature of interest with distinct edges on a specimen. Use a
combination of contrast, brightness and magnification adjustments to
maximize the imaging quality.
1. When the mouse cursor is over an imaging area, right-press (the
mouse cursor changes to a double-ended arrow). Move the mouse
from side to side until the selected quad imaging is sharp, then
release the mouse.
Note: 
Magnification changes during focusing but returns to the original
value after mouse button release.
2. The focus function (cursor) is active over the whole screen without
any interference with other controls. If the full mouse motion is not
sufficient to get the focus: release the mouse at one side of the
screen, move the mouse cursor to the opposite one and right-press
again (over an imaging area) to continue focusing.
3. If this is a new specimen first time focusing, run the Link Z to FWD
function (see Chapter 3).
Focusing at a higher magnification makes the result more precise. For
example, for an output at the 2000× magnification focus at 4000× –
8000× magnification.
To avoid scanning too long and contaminating or even damaging the
sample before you take the final image, move away from the feature of
interest with the X and Y stage controls, and focus until the image is
sharp on an adjacent area.

Focusing with MUI (option)

Use coarse and fine focus knobs. The imaging immediately responds to
the MUI.
Note: 
Use also the following functions to focus 
(see Chapter 3): Reduced area (F7), Auto Focus (F11).

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Operating Procedures: Imaging Optimising

CORRECTING ASTIGMATISM
This optical aberration is caused by different focal lengths for rays of
various orientation, resulting in a directional imaging blur (X and Y rays
are not focused to the same plane on the edges).
There are special coils serving to correct this imperfection, which is
usually better visible at higher magnifications (3000× or more). You need
to correct astigmatism when you change the imaging conditions.
1. Focus an image.
2. Bring the imaging just slightly out of focus. The imaging appears to
become sharper in one direction whereas in perpendicular direction
blur increases (blurring or stretching).
3. Bring the imaging just slightly out of focus in the other direction to
observe the opposite directional blur.
4. Focus to the midpoint between the two directions, where the blur is
visible.
5. Use the Beam module / Stigmator 2D control.
The Mouse: shift + right-press while in the selected quad. This results
in a 4 arrowed cross appearing on the screen with the cursor position
at its center. Move the cursor around the screen to achieve maximum
sharpness. When you are satisfied, release the mouse.
The MUI (optional): adjust imaging sharpness with the stigmator X
and Y knobs until the best result is achieved. The computer beeps
when the stigmator limits are reached.
6. Repeat steps 1–5 as necessary.
If astigmatism is severe and the cross is close to the edge of the screen
when nearing correction, release the mouse and reposition the cross in
the center of the screen. Then repeat the procedure above to perform
further astigmatism correction. You can use reduced area
advantageously (see Chapter 3).
If astigmatism cannot be corrected, there may be some other reason,
usually an aperture is dirty (see Chapter 6), the magnification may be too
high for the beam spot size (see below) or the sample is charging (apply
conductive layer).

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 Operating Procedures: Imaging Optimising

DIRECT ADJUSTMENTS (CTRL + F8)

This is tabbed window for fine-tuning the beam geometry to achieve the
best focus and brightness.
Note: 
Ion beam Direct Adjustments are available only for accelerating voltages
under 8.06 kV.

Ion Beam tab

• The Quad 2D box minimizes the objective imaging shift during
focusing.
• The L2 Modulator button starts automatic L2 voltage oscillation
(periodically under- and over focuses imaging in a narrow range) to
facilitate the process.
Try to bring the rotation center to the screen center (if the
magnification is too high, the rotation could seem like a linear motion
instead of a rotation).
• The Amplitude slider sets the modulation amplitude. 









Ion Stigmator Centering tab

• The Stigmator Sin / Cos 2D box sets the astigmatism lenses to bring
the beam into the center. The crosshair indicates the actual stigmator
setting. This minimizes imaging shift during astigmatism correction.
• The Modulator Sin / Cos button starts modulation of stigmator
lenses in X / Y axis.
• The Amplitude slider sets the modulation amplitude.

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Operating Procedures: Imaging Optimising

Electron Beam tab

Model difference: 
Helios NanoLab 600i does not have the UC 2D Box.
• The Source Tilt 2D box corrects an imaging illumination drop by
changing an effective angle of the beam coming from the gun area
into the electron column.
• The UC Centering 2D box centers UC beam through U-mode
aperture.
• In the Crossover mode (activated with the button) the imaging shows
the electron source instead of the sample surface.
• The XOver Zoom slider set the Crossover image magnification.
• The Lens Align 2D box minimizes the objective imaging shift during
focusing. The 2D control indicates an actual beam position setting
relative to the final lens aperture.
• The Lens Modulator (useful for HV > 3 kV) / HV Modulator (useful
for HV < 3 kV) button starts automatic objective current / voltage
oscilation (periodically under- and over-focuses imaging in a narrow
range) to facilitate the process.
Try to bring the rotation center to the screen center (if the
magnification is too high, the rotation could seem like a linear motion
instead of a rotation).
• The Amplitude slider sets the modulation amplitude. 


Electron Stigmator Centering tab

• The Stigmator Center X / Y 2D box sets the astigmatism lenses to
bring the beam into the center. The crosshair indicates the actual
stigmator setting. This minimizes imaging shift during astigmatism
correction.
Try to bring the rotation center to the screen center (if the
magnification is too high, the rotation could seem like a linear motion
instead of a rotation).
• The Modulator X / Y button starts automatic stigmator electrodes
voltage oscilation (periodically changes under- and over- stigmator
setting in a narrow range) to facilitate the process.
Try to bring the rotation center to the screen center (if the
magnification is too high, the rotation could seem like a linear motion
instead of a rotation).
• The Amplitude slider sets the modulation amplitude.

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 Operating Procedures: Imaging Optimising

DIGITAL IMAGING ENHANCEMENT / 

IMAGING MIXING / COLORING
The Enhanced Image module offers various digital image
enhancements.
Note: 
When saving the image with the digital enhancements applied, be sure
to choose the correct file format (see below).
The LUT (Look-Up-Table) Tab
enables to monitor and modify a grey level distribution (histogram).
• The Presets list box enables to select the Digital Contrast, Digital
Brightness and Gamma values using pre-defined or custom presets.
• The D. Contrast continuous adjuster sets a contrast in the range
from -10 to +10 (negative values lead to an inverse imaging).
• The D. Bright. continuous adjuster sets a brightness in the range
from -2.0 to 2.0.
• The Gamma continuous adjuster corrects image brightness non-
linearly in the range from -10 to +10.
• The Graph window graphically displays (blue line) an applied
modification. Original / modified values are on the horizontal / vertical
axis.
• The Histogram button switches on / off the grey level distribution
(corresponding to the active quad image) display. The left / right side
corresponds to black / white original image pixels. The height of the
red line is proportional to the number of pixels with the corresponding
gray value.
• The Save button saves the actual setting as the custom preset.
• The Default button restores the default values.
• The Undo / Redo button cancels / applies again the last changes.
The Mix 3 / Mix 4 Tab
The Mix feature operates in quad 3 / quad 4 and are enabled only if the
Detector menu / Mix is selected for a quad 3 / 4. It uses the processed
images (Average / Integrate, Digital Contrast, Digital Brightness, Digital
Zoom), not the raw detector signals. Any combination of live and paused
images can be mixed together, providing all mixed images have the
same pixel resolution. However, there are some logical limitations and
behaviours:
• The Average and Integrate filters are disabled.
• Pause / Resume influences the mixed image only, not its sources.
The Mix quad is always paused immediately regardless of the actual
scanning status.
• The CCD image is not mixed.
Note: 
In the Mix 3 tab the Source 3 controls and the Select 1+2+3 button are
disabled.
• The Presets list box enables to select the mixing ratios and colors
using pre-defined or custom presets.
• The Source 1 / 2 / 3 linear continuous adjuster tunes the mixing ratio
of quad 1 / 2 / 3 images. The adjuster % values shape
correspondingly the resulting image. Changing any Source value
influences the other ones automatically to reach the 100% sum.
• Clicking the Color control areas (below each Source adjuster)
enables to select a color, replacing the source image black (left) /

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Operating Procedures: Imaging Optimising

white (right) one. The image gray scale is linearly transformed to a

new color spectrum before it is mixed with other image(s).
Note: 
Color images (see below – the Color tab) are converted to greyscale
ones before mixing.
• The Invert check boxes inverts the corresponding source image
spectrum. It has the same effect as exchanging the left and right
colors selection.
• The Select 1+2 / 1+2+3 button selects between quads 1+2 or quads
1+2+3 mixing modes.
• The Save button saves the actual setting as the custom preset.
The Color Tab
enables to colorize a gray scale imaging. An imaging already colored
with the use of the Mix 3 / Mix 4 tab cannot be colored again, the Color
tab is disabled.
• The Presets list box enables to select the color profile using pre-
defined or custom presets.
• The Coloring Control area displays the active quad image histogram
and enables to create a color profile.
Right-clicking into the histogram area adds the vertical borderline with
a divided triangle on top (right-clicking onto an existing one removes
it). Pressing and dragging a borderline changes its position along the
histogram. Clicking onto the left / right part of the triangle selects the
left / right border color. The imaging gray scale between two
borderlines is linearly transformed to a new color spectrum.
• The Hand button enables to select and color a particular image gray
level. Clicking it opens the color selection dialogue: select a color and
press the OK button. The mouse cursor changes to the hand image.
Click the feature image you want to highlight. New borderline is
added into the histogram with a rectangle on top. The selected grey
level is marked with the chosen color. You can move this borderline
and change its color the same way as a borderline with a triangle on
top. By dragging the rectangle left / right side the highlighted grey
level range could be changed.
• The Enable check box switches on / off actual color settings for the
active quad image.
• The Save button saves the actual setting as the custom preset.
The Process Tab
Here the user can set parameters, which adapt image when clicking the
Apply button, or when selecting the Tools menu / Image Post
Processing (Ctrl + F7). The Undo button, or the Tools menu /Undo
Image Post Processing (Ctrl + Shift + F7) reverts the corrections back.
• The Denoising strenght (0 / 1 / 2 / 3 / 4) removes dust and scratches
from the image.
• The Sharpening strenght (0 / 1 / 2 / 3 / 4) corrects the imag7e
sharpness.
• The Undo / Redo button applies the processing again.
• The Undo / Redo button cancels / applies again the last changes.
The Custom settings could be saved.
Note: 
This functionality works only with greyscale images (not colored via
Color tab), images which are paused or with loaded saved ones.

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 Operating Procedures: Standard Detectors

Standard Detectors

EVERHART THORNLEY DETECTOR (ETD)

It is a scintillator photo-multiplier type detector collecting electrons
generated by the primary beam interaction with the specimen surface. It
is permanently mounted in the chamber over and to one side of the
sample. It works in Modes:
• Secondary Electrons (SE)
• Backscattered Electrons (BSE)
• The Deceleration Mode is available, when it is on (see below)
• Custom

ETD Settings
The Detector Settings / Mode list box enables to choose a SE / BSE
mode (the Grid Voltage is set to +250 V / -150 V) or a Custom mode, for
which the Grid Voltage could be set by the adjuster in a range from -240 to
+ 260 V. When the voltage is negative (use a range of -25 to - 240 V), SE
are repelled from the ETD detector and only BSE are detected.

THROUGH LENS DETECTOR (TLD)

The TLD is primarily designated to high resolution imaging in the SEM
Mode 2 at which one can choose Modes:
• Secondary Electrons (SE)
• Backscattered Electrons (BSE)
• Charge Neutralization: suction tube voltage is set to zero
• Down-hole visibility: suction tube voltage is set to the highest value
• Custom
• Deceleration Mode is available, when it is on (see below)

TLD Settings
• The Suction Tube Voltage adjuster enables to modify electron
collection. When the voltage is negative, low energy secondary
electrons are repelled from the TLD detector and only backscattered
electrons are detected. When the voltage is positive, low energy
secondary electrons are collected by the TLD detector. The Suction
Tube Voltage capability is from -150V for only backscattered electrons
to +150V for secondary electrons collection.
• The Mirror adjuster deflects the acceleration path of the SE’s into the
detector in Secondary Electrons mode. It also can be used to convert
high energy BSE’s to SE’s in Backscatter Electron mode.
Note: 
When using the FIB Immersion utility (see Chapter 3) the Custom Mode
Suction Tube Voltage for electron imaging is copied to the Custom mode
for ion imaging.

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Operating Procedures: Standard Detectors

SECONDARY ION / ELECTRON DETECTOR (ICE)

The ICE is a charged particle detector mounted near the end of the ion
column. It collects secondary ions (SI) or electrons (SE, BSE) to form an
imaging signal.
The Electron beam and Ion beam imaging (which is distinguished by the
beam icon in the module header) have different Modes.
Electron beam modes:
• Secondary Electrons (SE)
• Backscatter Electrons BSE)
• Custom
• Deceleration Mode – available, when the Deceleration Mode is on
(see below)
Ion beam modes:
• Secondary Electrons (SE)
• Secondary Ions (SI)
• Custom

ICE Detector Settings

When changing any of the adjuster, the Custom mode is activated for
any beam, enabling to change values.
• The Grid continuous adjuster: positive voltage for SE imaging,
negative voltage for BSE and SI imaging
• The Converter continuous adjuster: 0 for SE and BSE imaging,
negative for SI imaging
Note: 
Changing the beam current adjusts the detector contrast automatically.

ICE & ETD COLLECTION EFFICIENCY

ICE and ETD detectors are both able to collect SE signal. In order to
prevent the inactive (paused) SE detector from taking the SE signal, set the
Preferences dialogue / General tab / Optimized collection efficiency
item to Yes, which provides more SE signal to the active SE detector. This
is advantageous for common imaging but it is not recommended to use
while patterning, because image quality decreases in SPI and iSPI mode.
Note: 
Large changes to the custom conditions on biased detectors (such as
the ETD and the ICE) could cause beam shift, which in turn affects the
coincidence of the two beams. Therefore it is not advisable to change
custom conditions while patterning (if coincidence is affected then re-
calibration is necessary before starting to pattern).

INFRARED CCD CAMERA

Imaging obtained with this camera assists in overall sample and stage
orientation by enabling to view the inner space of the specimen chamber
(an optical quad). It protects the objective pole piece and retractable
detectors against collision when moving (especially in the Z-direction) or
tilting the stage. IR LED’s are used to light the specimen chamber interior.

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 Operating Procedures: SEM Imaging Modes

SEM Imaging Modes

The electron column can be operated in three different final lens modes,
two electron source modes and in the Beam Deceleration mode.

FINAL LENS MODES

These modes can be selected in the Beam menu / SEM Mode or directly
from the toolbar.

• Mode 1: Field-Free
This is the default survey mode essential for navigating and reviewing
samples at lower magnifications and for observation of ferromagnetic
samples. The immersion lens is switched off and the default detector
is the ETD in Secondary Electron operation.
• Mode 2: Immersion
This mode is used for ultra-high resolution imaging of the sample.
The immersion lens is switched on and the default detector is the TLD
in Secondary electron operation.
Caution! 
Never switch to the Immersion lens mode with a magnetic specimen
in the chamber!
• Mode 3: EDX
This mode is used for EDX / WDX analytical tasks with EDX detector
w/o magnetic collimator. The Immersion Lens is not so powerful as in
Mode 2 but can act as an electron trap for backscattered electrons to
improve X-ray collection.
Selecting Mode 2 and 3 have their’s own Beam menu presets.

ELECTRON SOURCE MODES

This mode can be switched on in the Beam menu / UC On item.
Model difference: 
Helios NanoLab 600i does not have the UC On and UC Auto items.
• In the Normal mode (UC On not ticked) the full system HV and beam
current range is available.
• In the UniColor mode (UC On ticked) maximum HV is 10 kV and
maximum beam current is 25 pA. Electrons are supplied with the
energy spread less than 0.2 eV, which improves image quality at low
HV and low beam currents.
Ticking the UC Auto switches UC-mode on automatically, when HV
and beam current values are in the allowed range.

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Operating Procedures: SEM Imaging Modes

BEAM DECELERATION MODE

Model difference: 
BD is option for the Helios NanoLab 600i.
The Beam Deceleration mode (BDM) method is based on a negative
voltage Stage Bias (bias) applied to a stage (i.e. a sample). The
electrical field between the sample and the nearest surface over (a
column bottom or a detector) is formed, acting as the additional
electrostatic lens. Its power is described by the Immersion Ratio
(imRatio) parameter (see below).

Detection Principles
The Beam Deceleration influences both primary and signal electrons.
As the sample is at the negative potential according to the ground and
detectors, the initial SE and BSE energy (when leaving the surface) is
accelerated by the Stage Bias before the detection. The higher is the
Immersion Ration, the lower is the difference between SE and BSE
energies when detected.
Signal electrons are accelerated upwards and deflected towards the
column axis. The SE have a low initial speed and they are usually
absorbed into the detector central hole, equally like the BSE heading
upright. Conversely the BSE heading nearly parallel to a surface (which
normally cannot be detected) are driven to a detector.
By changing the Stage Bias an output angle distribution of electrons
leaving a surface could be obtained.

FIGURE 5-2 TYPICAL TRAJECTORIES OF SECONDARY (RED)

AND BACK SCATTERED (GREEN) ELECTRONS

Detectors most convenient for the Beam Deceleration are BSE ones,
placed closely under or directly inside the column. Their efficiency
depends on their active area: the smaller the active area inner diameter
the better. The standard ETD could also be used, but its efficiency is low.

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 Operating Procedures: SEM Imaging Modes

Beam Deceleration Applications

• The BDM enables detection of the BSE when the electron energy is
under the detection limit of the detector.
• The BDM expands the electron energy range under the minimum HV
limit.
• The BDM improves the microscope resolution at low accelerating
voltages. A conventional microscope resolution is limited by a
chromatic aberration at low electron energies. The higher is the
Immersion Ratio, the smaller are the aberrations and a loss of
resolution at low electron energies is well compensated.
• The BDM enables to detect electrons heading nearly parallel to a
surface which accentuates a surface roughness.
Application Restrictions
• The sample tilt causes an electrical field deformation, which adds not
correctable aberrations (a chromatic aberration and an image
distortion). An acceptable sample tilt is about a few degrees, for a
higher immersion ratios preferably less.

FIGURE 5-3 SIGNAL DISTORTION AND IMAGE ABERRATIONS

FOR TILTED AND ROUGH SAMPLE (TIN BALLS) 
AT HIGH IMMERSION RATIO

Beam Deceleration Module

The Beam Deceleration module has following features:
• The On button switches the BDM on / off. This is available only with
the Beam On. When switching the beam off, the BDM switches off too
automatically.
• The Stage Bias (bias) reflects the negative voltage applied to a
stage. Minimal value is 50 V, maximal is 4 kV.
Note: 
It is possible to control the stage bias by the active image databar
menu (see Chapter 3).
When the BDM is on, a hook mark is placed behind the HV. In this case
this value represents energy of electrons reaching a sample surface (it is
also stored within the TIF file header).
The imRatio = (HV + bias) / HV.

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Operating Procedures: SEM Imaging Modes

Beam Deceleration Mode Imaging Procedure

1. Put the sample into the chamber and pump.
In the BDM a sample becomes the electrode. Its position, size, tilt and
surface roughness influence an imaging quality. At optimal conditions
the sample should be symmetrical, planar, have a size comparable
with the detector size, and placed perpendicular to the column axis. In
other conditions a distortion, an astigmatism and a blurring caused by
the chromatic aberration appear. This is even worse when the
Immersion Ratio is higher.
2. Select the suitable HV and find an area of interest. Set the Eucentric
Position (see above) and tune an imaging with the Beam menu /
Lens Alignment and the Beam module / Stigmator 2D control (see
Chapter 3). In various quads select the SE and BSE to observe
different imaging simultaneously.
3. Click the Mode On button. Gradually raise the Stage Bias, 
the SE / BSE image is getting dark / light.
At low magnifications an ETD image should become dark
symmetrically around the window center, in other case the sample
could be tilted.
When a dark area is shifted with an Stage Bias change, the sample is
possibly not parallel with the detector. With the use of the
Compucentric stage rotation / stage tilt try to keep the dark are in the
center of the screen.
Note: 
When the retractable vCD detector is inserted, stage tilt is restricted
via the UI. Override it by manual control to keep the dark area in the
center of the screen.
Note: 
An image shift when changing the Stage Bias could be caused by
imaging near the sample edge or any other edge.

4. Set the Stage Bias considering the sample material (charging

compensation, material contrast) and to optimize the signal. Set the
brightness, contrast and WD according to the requirement.
5. Tune the Beam menu / Lens Alignment and the Beam module /
Stigmator 2D control (both factors remembers the HV and Stage
Bias last used).
6. Repeat steps 4. and 5. to get the best result.

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 Operating Procedures: Capturing and Handling Single Image

Capturing and Handling Single Image

After obtaining a good image quality, the image could be paused and
saved. It is possible to save an image using the File menu or using the
Scandium database software (option) image saving function.
Setup the file name label and harddrive destination for the image to be
saved using the next available label / number prior to the capture
session. Set the databar information important for the archiving (see the
Preferences… / Databar tab).
The conditions for a good image quality are:
• Slow scan speed (longer dwell time) of the beam.
• Select a pixel resolution from the drop down list box to suit the detail
in the image, i.e. no tearing pixelated edges.
• Increase the magnification at least 2× above the desired value, focus
and correct the astigmatism (using the reduced area), then return the
magnification back.
• Use the Videoscope to set the Contrast and Brightness accurately,
otherwise use the Auto Contrast Brightness procedure.
• Use Pause / Snapshot / Photo / Active Preset Snapshot / filtering
functions (see Chapter 3).

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Operating Procedures: Capturing and Handling Single Image

IMAGE TYPES
A computer perceives an image as a two-dimensional array of numbers
– bitmap. Each array element is called a pixel and is represented as an
integer value. Frequently, the pixel is represented as an unsigned 8-bit
integer in the range [0, 255], with 0 / 255 corresponding to black / white
and shades of gray distributed over the middle values. A 16-bit
representation produces up to 65 536 different shades of gray (it is not
possible to distinguish onscreen), which may be crucial for obtaining
accurate data in analysis.
The raw scanned image is always a greyscale bitmap. The colors are
possible to add digitally as a result of particular features. The UI is able to
display and save images with a various bit depth:
• The Greyscale 8 / 16 bit image offers 256 / 65 536 levels of grey.
Live / Averaged and Integrated images are scanned as 8 / 16 bit
ones. For the Mix quad images a selection between the 8 or 16 bit
mode is possible.
• The Color 24 bit image offers 256 levels of each primary color (red /
green / blue).
Digital colors coming from the Display Saturation feature, from the
Image Enhancement module / Color tab, from the Mix quad with color
mode set changes an image bit depth so there is no way to save it
without them. When user wants to obtain the image without these
color enhancements, it is necessary to turn off the respective UI
functions.
Colored digital overlaid graphics (Measurement and Annotation) are
possible to be saved with / without an image (see the respective
checkbox in the Save As dialogue). Other types of overlaid graphics
over an image are never saved (icons, controls, etc.).

Digital File Formats

The image captured can be saved in various digital formats, depending
on the resulting color and bit depth needed. Generally there is no reason
to save an image with a higher bit and color depth than available in an
original one. Over against saving an image with a lower bit and color
depth than available leads to the loss of information. The message is
displayed in this case onscreen.
• The TIF 8 / 16 – greyscale image type
• The TIF 24 file – color image type
TIF file contains active processing information, which could be utilized
for a databar setting (see the Preferences… / Databar tab).
• The JPG file is a compressed file format employing a lossy
compression algorithm resulting in the small file size with a little loss of
information, depending on the particular image appearance and the
compression level (factory preset to 80%). The 8 / 24 bit depth is
automatically selected when saving the greyscale / color image file.
• The BMP file is an uncompressed file format. The 8 / 24 bit depth is
automatically selected when saving the greyscale / color image file.

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 Operating Procedures: Capturing and Handling Single Image

SAVING / OPENING / PRINTING

The following universal file handling functions could be used:
• Save (Ctrl + S) stores the image to the predetermined location with
the last used filename including an incremental number.
• Save As… opens a dialogue for saving images (this provides an
opportunity to change the file name, its location, and the possibility to
save also Databar and overlaid graphics). Both functions can be
linked to the Snapshot / Photo function (see the Preferences… /
Scanning tab).
• Save All... behaves the same way as Save As functionality, but
enables to save images from all four quads at once.
• Open… opens a single image file into the selected quad. The
dialogue displays, by default, the location used in the last Save As…
utilization.
• Print… (Ctrl + P) opens the printer setup dialogue so that the choice
of printer and settings can be established to print the selected quad.
Clicking the OK button in the printer setup dialogue activates the
printer to print the job.

Image Capturing Procedure

1. Select the area of interest and set the Magnification, the Scan
condition, the image pixel Resolution and the Databar informations
that are required in the saved image.
2. Make the best image using any suitable method you are familiar with.
3. Use the Pause (F6) / Snapshot (F4) / Photo (F2) / Active Preset
Snapshot (Ctrl + F2) function. The scan makes one screen / quad
pass (or several passes when the number of integrated frames is
larger) and pauses.
4. The image can now be saved by 
File menu / Save (Ctrl + S) / Save As… functions.

Image Printing Procedure

1. Select the area of interest. Set the Magnification, the Scan
condition, the image pixel Resolution and the required databar
informations.
2. Capture the image or open a saved one.
3. Click the File menu / Print… (Ctrl + P), a print dialog appears.
4. Complete the print setup and click the OK button.

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Operating Procedures: Recording Movies (Saving Multiple Images)

Recording Movies (Saving Multiple Images)

This function captures dynamic experiments performed with the

microscope and creates the digital video files (AVI). Up to 4 imaging
quads (not the optical one) can be recorded simultaneously with a
synchronized start. It is possible to switch between single and quad
image window while the video is recording. The movie has the following
embedded features:
• Resolution 768 × 512 or 1536 × 1025
• Databar image optionally included in the video
• Average or Integration changeable during recording
• Scan speed changeable during recording
• Reduced area pauses recording of all quads
• Remaining time indicator
• Single frame TIF images recordable during video sequence
• Compressed AVI (*.avi) formats
• Start, Stop and Pause onscreen indicators
• Preferences set-up dialogue
Note: 
For the quad(s) with the Enhanced Image module / Color tab / Enable
check box ticked, the Movie recording is paused, the colored TIF files
are stored anyway if selected (see below).

MOVIE TAB PREFERENCES DIALOGUE

The Preferences… (Ctrl + O) / Movie tab provides two modules, one to
set-up conditions for timing (labeled Timer), the other to set-up save
conditions for the resultant movie (labeled File).

FIGURE 5-4 MOVIE PREFERENCES

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 Operating Procedures: Recording Movies (Saving Multiple Images)

Timer module
The parameters in this section can be changed when the digital video is
inactive, but are disabled during recording. The digital video is recorded
asynchronously to the scanning.
• The Movie check box – AVI (Digital Video) timer: 
After the Delay time, the image of each active quad is stored
immediately (even in the middle of the frame) as a new frame in the
video stream.
• The TIF check box: 
After the Delay time, images series of each active quad are stored at
the end of the running scan (the system waits) in TIF format.
• In the read only area additional information are given about the
number of stills (frames) per time unit (seconds, minutes).
If both TIF and Movie check boxes are ticked, AVI and also TIF files are
stored. In this case the AVI file is not reconstructed from TIF files, which
means the directly recorded movie can be different from the movie
reconstructed from TIF files.
Note: 
TIF files are better to save in many cases as they can be built into a
faster AVI and the databar display can be customized when building an
AVI file (see below). 
If both AVI and TIF are recorded, the AVI may be jerky due to delays
when writing TIF files to a disk. TIF delay must always be longer than or
equal to the Movie delay.

File module
Names of Movie [TIF] files are composed as follows: 
File name, (quad name), Numeric seed, [- series number].avi [tif]
For example: MovieName (Quad1) 015 [- 00023]. avi [tif] 
[The series number always has five digits form with leading zeros.]
• The File Name – a generic file name must be entered here, otherwise
the Movie tab cannot be closed. Do not use punctuation, dashes or
other non alpha-numeric characters, otherwise the movie maker is
not able to build an AVI.
• The Save in – a path to an existing directory must be entered here,
otherwise the Movie tab cannot be closed. Use the Browse button to
find the location.
• The Numeric Seed – enter any number from 1 to 999 which is
converted to the three digit form with leading zeros. The numeric
seed is automatically incremented, after the recording has stopped,
or the video file size limit has been reached.
• The Video File Size – the maximum AVI video file size (lower than
2000) in MB must be entered here, otherwise the Movie tab cannot be
closed. After reaching this size, the video file is closed and a new one
is automatically created, without interruption of the recording process.
A warning dialogue appears if the hard drive lacks sufficient free
space.
• The File Type – the list box with supported video compression format
types. Try to change the format if the resulting movie files are too big or
if the system is overloaded during the movie recording.
• The Record Databar check box allows the databar to be included in
the video (tif files).

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Operating Procedures: Recording Movies (Saving Multiple Images)

RECORD MOVIE
The red dot button starts the recording of all active quads at the same
moment – no video / images are stored for paused quads. When a quad
is paused during the video recording, the storing of the video frames is
interrupted but the video streams keep synchronization for the next
recording.
When the red dot representing ‘Start’ is pressed, it turns to a red square,
representing ‘Stop’. Pressing the red square then stops the recording of
the video in all quads and closes all video files.
The red dot with the timer (displayed in the top right-hand corner)
indicates that recording is active in this quad. The Pause symbol
indicates that the record is running but the data from this quad are not
stored (the quad is paused).
The timer indicates the time estimation (in the hh:mm:ss format)
remaining to the end of the video. This is calculated from the average
disk space consumption and the disk free space.

Record Movie Procedure

1. Open the Preferences… / Movie tab. In the Timer module tick the
Movie or TIF check box and select the desired Delay time (the period
between stored frames).
2. In the File module fill in the File Name and give the Save in directory
path. Fill in the Numeric Seed value and the Video File Size. Select
the File Type and choose whether to record the databar with the
Record Databar check box.
3. Pause those quads which you don’t want to record. Set up the
imaging parameters in the live quad(s).
4. Select the File menu / Record Movie (a tick mark) or click the toolbar /
red dot button. When the scan resolution is higher than 1024 × 884 the
dialogue appears.

5. Choose either of the offered Resolution values at which the movie

starts to record.
6. Select the File menu / Record Movie again or click the toolbar / red
square button to stop the movie recording.

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 Operating Procedures: Recording Movies (Saving Multiple Images)

FEI MOVIE CREATOR

This is a separate program that creates a movie from a sequence of TIF
images. Click the Tools menu / FEI Movie Creator… to activate the
tabbed dialogues.
The following items are common for all tabs:
• The Databar Preview displays the databar created in the Databar
tab.
• The Status displays the progress of movie creation process.
• The Create Movie button opens the File tab and starts the movie
creation process from the TIF files to a single AVI file.
• The Stop button stops the creation process.
• The Close button closes the FEI Movie Creator program.

File Tab
FIGURE 5-5 FEI MOVIE CREATOR TAB: FILE

• The Name Prefix – click the … button to browse the TIF files (with the
desired sequence prefix) directory. It is not necessary to choose the
first file in a row.

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Operating Procedures: Recording Movies (Saving Multiple Images)

FIGURE 5-6 BROWSE DIALOGUE

• The Time Period – select the ms radio button to select a custom

timing for the movie playback. One may experiment (200 ms is good
for most movies to speed it up). Select the TIF Time radio button to
select a real timing for the movie playback.
• The Gray Movie button suppresses the colors in the resulting movie.
• From / To – enter the number of the starting / ending frame. This field
is filled automatically with the first / last frame available.
• Save in – enter the path where the AVI file should be saved. Click the
… button to browse it.
• File Name – enter the resulting AVI file name. This field is filled
automatically with the first image file name.

Databar Tab
Settings made in this dialogue does not affect the databar or units
settings used in the xTUI.
Note: 
The Databar Preview does not show any item until you enter the File
tab / Name Prefix field.

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 Operating Procedures: Recording Movies (Saving Multiple Images)

FIGURE 5-7 FEI MOVIE CREATOR TAB: DATABAR

• The Available / Displayed items: lists – all items that can be entered
in the databar / are already present in the databar.
• > / >> (< / <<) buttons adds one / all item(s) from the Available list to
the Displayed list (removes one / all item(s) from the Displayed list
back to the Available list).
Since there is a finite amount of the databar space, the area expands
or contracts as other items are added to or removed from the
Databar. The item exceeding the allowable space is ignored.
• Move Up / Move Down / Top / Bottom buttons move a position up /
a position down / to the top / to the bottom in the Displayed list (a
position to the left / a position to the right / to the left / to the right in the
Databar Preview).
• The Label / Show Beam Icon / Micronbar check boxes set the
display of the appropriate items in the Databar. The Micronbar scales
to the magnification.
• The Units… button sets the Units of Measure / Pressure /
Temperature used in the movie Databar display.

Preview (tab)
Once the movie is set-up, opening the Preview tab automatically
displays the first image of the movie sequence.

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Operating Procedures: Recording Movies (Saving Multiple Images)

FIGURE 5-8 FEI MOVIE CREATOR TAB: PREVIEW

• The Start / Pause / Stop button starts / pauses / stops the movie play
back. By dragging the adjuster one can run forward or backward
through the movie.

PLAYING A MOVIE
The AVI file movie can be played in the Windows Media Player or any
another more advanced movie editing program recognising the *.avi file
type.

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 Operating Procedures: Stage Control

Stage Control

EUCENTRIC POSITION
Establishing the eucentric height is an important part of setting up a
sample for observation or modification.
At the eucentric position, the stage tilt and the beam axes intersect. When
the stage is tilted or rotated in any direction, this point remains focused
and almost does not shift. At the eucentric position, one can use various
system components in a safe and optimal way (e.g. GIS, Omniprobe).
Eucentric position should be adjusted after loading any new sample, as
the sample loading clears all position information.
Note: 
For electron imaging of non-tilted sample the eucentric position
adjustment is not necessary. But it is still required to run the Link Z to
FWD procedure (see Chapter 3).

FIGURE 5-9 EUCENTRIC POSITION PRINCIPLE

Beam Beam

Eucentric position
Eucentric position
Point of interest
Point of interest

Stage
Stage Tilt

1) The point of interest is focused below the Eucentric 2) Tilting the stage moves the point of interest out of the
point (see 2). beam.

Beam Beam
Eucentric position 
Pont of interest  and Point of interest
is at eucentric position.

Stage
Stage Z adjustment

3) The point of interest is focused at the Eucentric point 4) Tilting the stage does not move the point of interest out
(see 4). of the beam.

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Operating Procedures: Stage Control

Setting Procedure
1. Apply the Stage menu / Auto Beam Shift Zero function.
2. Display the Window menu / Center Cross (Shift + F5).
3. Focus an image. Link Z to FWD and go to 5 mm WD.
4. Set stage tilt to 0°.
5. Using the Z-control, coarsely focus the image.
6. Set the magnification to 1000x, find a recognizable feature and center
it under the yellow cross by moving the stage.
7. Watching the feature, change the stage tilt to 10°. 
Using the Z-control, bring the feature back under the cross.
8. Change the stage tilt to -10°, and bring the same feature back under
the cross using the Z-control.
9. Change the tilt to 0°. The feature should not shift significantly. 
If the shift is > 5 µm, repeat steps from No. 6 to No. 9.

SOFTWARE CONTROL
Helios NanoLab 450 / Helios NanoLab 650 / Helios NanoLab 600i
The Navigation page / Stage module controls the stage movements that
locate the position of the specimen by reference to coordinate points. It
consists of Map / Coordinates / Tilt Correction tabs.

Map tab
In the map area the stage schema is represented displaying all stored
locatable positions, which are listed in the Location list box for selecting.

FIGURE 5-10 MAP AREA ELEMENTS

2 6

9
7
10 1

4
8

TABLE 5-2 MAP AREA ELEMENTS

No. Function
1. Black +: mechanical stage center.
2. The darker rim: the sample holder outline.
3. Light grey dashed line: physical limit of the stage
movement along X and Y axes.
4. X / Y scroll bar: to move the stage schema area in a X / Y
(stage) direction at different magnification factors.
5. Magnification factor of the map area (1x–100x).

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 Operating Procedures: Stage Control

TABLE 5-2 MAP AREA ELEMENTS

No. Function
6. Radar view: 
Black triangle: the moveable rotation angle positioner. 
Grey perpendicular lines: denote rotation position. 
Grey +: stored positions as on the map. 
Red + in a red circle / Blue +: positions as on the map.
7. White × on a red background: a stored location with the
rotation noted by the black key position.
8. Red + in a red circle: the actual active position.
9. Blue +: a new location not stored.
10. White + on a green background: indicates a stored
position highlighted in the location list.

Radar view
The small circle in the stage schema top right corner conveys the stage
rotation at any time by the black triangle and perpendicular lines position.
To rotate the stage, press on the circle perimeter triangle. Move it round
and release the mouse at the desired position – the stage rotates
accordingly.
Location area
The Location list shows the Current Position and the Last Position
(the stage position before any movement) as default. When expanded, it
shows the positions list with a scrollbar.
Double-clicking anywhere in the circle area marks a new location (9) and
moves the stage to it.
The position selected becomes the actual active position and it is
highlighted in the list and also on the map (8).
Clicking a position name allows an user to edit it. Pressing the Enter key
or clicking a different item confirms the new name, pressing the Escape
key restores the old name.
• The Open button opens a stored Stage Map file (stg).
• The Save button saves a Stage Map file to disk.
When closing the UI the system registry automatically keeps the
Stage Map file with the specific User name to be loaded after the log-
in procedure.
• The Clear button clears the existing Stage Map file including the
Location list.
It is possible to load / save stg file also with the use of File menu / Import
/ Export functions (see Chapter 3).

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Operating Procedures: Stage Control

Map Menu
Right-clicking over the Map area, provides the drop down menu.

FIGURE 5-11 THE MAP DIALOGUE

• Clicking the Add current stage position item adds a new Location
list entry, using the actual active position. The new entry is named
Position X (X = 1, 2, 3…). If a name already exists (because an user
loaded a Map list from a Stage Map file), the value is heightened until
a unique name is obtained.
The Coordinates tab / Add button has the same functionality.
• Clicking the Update to current stage position item stores the
(edited) coordinate values under the selected name (an overwriting
confirmation dialogue appears).
The Coordinates tab / Update button has the same functionality.
• Clicking the Remove selected position item deletes the selected
location(s) from the map and from the Location list.
The Coordinates tab / Remove button has the same functionality.
• Clicking the Magnification item provides a menu allowing the Map
area magnification factor (5) to be selected. Scroll bars (4) appear if
necessary to move over the whole Map area.
• The Center view item brings the selected location to the center of view.
• When the Auto center on target item is ticked and the Magnification
factor is used, the active location remains in the center of view.
• The Show radar view item switches the radar view display in the
map area On / Off.
• The Zero radar view item resets the stage rotation to 0°, which is
represented by the black triangle 12 o’clock position.
• The Show notch item switches the blue triangel display in the map
area On / Off, giving a quick view about the stage rotation.
• The Stage location overlay item toggles the detector and chamber
door position display in relationship to a sample.
• The Display map in Navigation Quads item switches the stored
positions display in naviagtion images.

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 Operating Procedures: Stage Control

Coordinates tab
Three modes are possible via the list box:
• The Actual mode (default) displays actual position coordinates in the
edit boxes.
• The Target mode activates when clicking a stored position or when
editing a coordinate value.
• The Relative mode is used to move stage by a given value and to
repeat it several times if needed.
Clicking the Go To button drives the stage to a new location. This only
acts on just edited coordinates (with a tick mark). Pressing the Enter key
after editing of any coordinate value works as the Go To button short-cut.
Double-clicking a stored location moves the stage to the desired position
immediately.
During the stage motion the Go To button changes to the Stop button,
which stops the stage immediately.
Coordinates X, Y, Z, R, T
Edit boxes for X, Y, Z, R and T coordinates are filled with the selected or
actual position values. The value changed is automatically ticked.
Caution!
• Danger of hitting the pole piece! The Link Z to FWD procedure did
not pass (see Chapter 3). The red arrow next the Z axis alerts the
positive Z-axis stage moving direction is up. It means raising a value
in the Z axis edit box causes moving the stage up towards the pole
piece.
• After running the Link Z to FWD procedure the symbol and the stage
moving direction changes. The black arrow next the Z axis indicates
the positive Z-axis stage moving direction is down.
The units of measure follow the Preferences… / Units setting, unless
the Stage menu / User Units function is active, in which case UU is
displayed for X and Y.
The software locks prevent inadvertent stage movement of selected
axes during particular applications. The edit boxes for locked axes are
disabled and the stage does not move in these directions. When any or
all axes are locked the Status module displays a closed lock instead of
an open one. By default all axes are unlocked.
When any axis is locked and the stage movement is required in that
direction (trying to move to the stored position), the warning dialogue
appears.
When the Compucentric: Rotation check box is ticked, the R
coordinate operates as the Compucentric Rotation function.
In case the Compucentric: Tilt check box is ticked and the stage is
tilted, the system compensates for observed sample point shifting during
a stage Z-axis movement with a stage Y-axis movement.
Note: 
Because this functionality invalidates the stage eucentric position setting
(see above), do not check the Compucentric: Tilt check box when setting
it!
Note: 
The R coordinate is permanently locked and its homing is disabled when
the heating or cooling stage is plugged in.

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Operating Procedures: Stage Control

Tilt Correction tab

When the appropriate check box is ticked, the function becomes active.
• The Dynamic Focus check box ticked – the focus automatically
changes as the beam scans from the image top to its bottom, trying to
follow the tilted specimen working distance change.
• The Tilt Correction check box ticked – the flat specimen
foreshortening compensation is on (in one direction, at a known tilt
angle, when the tilt axis is parallel to the stage XY plane).
Because the image is a two-dimensional representation of a three-
dimensional object, certain distortions occur. For instance, a square
grid image appears rectangular when you tilt the specimen. This
function corrects the aspect ratio and restores the square
appearance.
• The Automatic check box – switches between automatic and manual
tilt angle settings. If ticked, the Tilt Angle is equal to the stage tilt plus
the Specimen Pre-tilt linear adjuster value (a Tilt Angle correction in
case the specimen is not parallel to the stage XY plane).
• The Manual linear adjuster enables to manually set the Tilt Angle
from -90° to +90°. It is useful when the Dynamic Focus with Automatic
Tilt Angle does not give satisfactory results (or cannot be used at all
because the specimen is tilted in direction different from the stage
Tilt).
When switching from Automatic to Manual mode, the actual Tilt Angle is
not changed. When switching to Automatic mode, the Tilt Angle is set to
the actual stage tilt.
If the Dynamic Focus is on and the Tilt Angle is non-zero, an indicator is
displayed in the optical quad.
Notes: 
Both Dynamic Focus and Tilt Correction work properly only if the
specimen (scanned area) is tilted around the X-axis (in the same
direction as the stage Tilt). Therefore they cannot be used with Automatic
Tilt Angle in combination with a non-zero Scan Rotation. If the specimen
is tilted in a different direction, you have to align the tilt axis horizontally
using the Scan Rotation and then optimize the image focus by tuning the
Manual Tilt Angle.
Both functions are also disabled (check box cleared) in the Crossover
mode.
Due to the limited range of the dynamic focusing, the overall conditions
should be in certain limits. If the dynamic focus would be out of the
range, the checkbox becomes disabled. To enable it again, you can try
one or more of these actions: decreasing the Tilt Angle, increasing the
magnification or the working distance, decreasing accelerating voltage or
switching the Tilt Correction on (this helps especially at high tilt angles).

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 Operating Procedures: Stage Control

SOFTWARE CONTROL
Helios NanoLab 450S / Helios NanoLab 450ML
Microscope models equipped with the Flip Stage have the Navigation
page / Stage module consisted of Bulk / Flip / Tilt Correction tabs.
Active stage (Bulk or Flip one) is highlighted by a green tab header. 
Most elements corresponds to ones mentioned above.

FIGURE 5-12 THE STAGE MODULE

Bulk tab
The Bulk tab allows to control the Bulk stage similarly to the Map and
Coordinates tabs control.

Flip tab
The Flip tab contains particular functions to operate the Flip stage:
• ZF represents the Flip stage Z-coordinate.
• AF (Alpha Flip) represents a Flip stage tilt (from -55° to 100°).
• T represents Bulk stage tilt (from -3° to 60°).
• View Y-Z shows the row holder arm schematically at the eucentric
height (blue line marker, WD = 4 mm) with the tilt angle 0° (black
contour).
Helios NanoLab 450S
• View X-Y shows a selected row holder grid position. Doubleclick a
required grid position to quickly move the row holder in X-axis
direction. 
The Flip stage X / Y move is restricted compared to Bulk stage.
• The Load/unload Position button moves the stage to a row holder
exchange position.

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Operating Procedures: Stage Control

HARDWARE CONTROL

Manual User Interface (MUI)

Model difference: 
MUI is option for the Helios NanoLab 650 / Helios NanoLab 600i.
The MUI provides knobs to perform functions that can also be performed
with the software. It is connected to the USB connector located on the
microscope controller.

FIGURE 5-13 MUI

The MUI offers additional flexibility for controlling magnification, beam

shift, focus, astigmatism, contrast and brightness.

Joystick
Model difference: 
Joystick is option for the Helios NanoLab 650 / Helios NanoLab 600i.
The Joystick provides knobs to perform functions that can also be
performed by the software. It is connected to the USB connector located
on the microscope controller.

FIGURE 5-14 JOYSTICK

• The Up / Down lever motion moves the stage in Y axis.

The Left / Right lever motion moves the stage in X axis.
The Left / Right lever rotation rotates the stage left / right.
• The button 1 is not used.
• The button 2 is used together with the lever motion:
- Up / Down moves the stage up / down 
(regardless the Link Z to FWD status). 
- Left / Right tilts the stage left / right.
• The button 3 speeds up the stage motion:
- 10× in X / Y axis 
- 5× in Z axis 
- 2× in R / T axis

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 Operating Procedures: Stage Control

STAGE RELATED FUNCTIONS

Stage Movements – Keyboard Shift

The stage can be moved about 80% of the field of view in perpendicular
direction by clicking the appropriate keyboard Arrow key (with the Shift
button pressed simultaneously about 40%).

Stage Movements – Track

This function allows continuous directional stage movements at a
variable speed.
Wheel-press over an selected electron image quad – the yellow dot
appears onscreen at the mouse cursor point. Move the mouse to the
direction intended for an observation – an yellow arrow appears
onscreen denoting the direction opposite to the stage motion. The
motion speed raises with the distance between the arrow and the dot,
the direction can be changed by moving the mouse. When you come to
the place of interest, release the mouse wheel – the action stops.
In the second possible mode the mouse wheel does not need to be held,
just click it to start the Track motion and click it again to stop it.

FIGURE 5-15 TRACK FUNCTION

In the optical quad pressing the mouse wheel activates the stage Z
movement, which can be seen live.
• When Wheel-pressed, moving the mouse up / down moves the
stage up / down (Z-coordinate).
• When Ctrl + Wheel-pressed, moving the mouse left / right tilts the
stage left / right.
The direction is indicated by a yellow arrow, either pointing up / down
from the horizontal line or left / right from the vertical line.

Stage Movements – Get

This function brings an image point of interest to the screen center.
Double-click an image point. The object is mechanically centered
onscreen by moving the stage, which is suitable for lower magnifications.
When working at higher magnifications, beam shift could be also
employed (see the Preferences… / General tab). In this case the object
is electronically centered onscreen by moving the electron beam. When
the beam shift comes to a limit in any direction, its value resets and the
necessary stage movement adapts the observed point position.

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Operating Procedures: Stage Control

FIGURE 5-16 GET FUNCTION

Beam Shift
When you want to employ the beam shift only (which is suitable for
higher magnifications), click an image point while holding the Shift
button pressed. The Hand cursor allows to move the image area in any
direction.
When the limit of the beam shift has been reached, either the Stage
menu / Auto Beam Shift Zero or the Beam Shift Reset function needs
to be applied (see Chapter 3). In this case the beam shift is reset and the
observed point position is adapted by the stage movement.
Releasing the mouse stops the action.

xT Align Feature…
This utility is designed specifically for long features, extending off the
screen at the magnification required for an observation. It applies the
mapping process bringing the long feature either to the horizontal or
vertical axis to make the navigation easier. This can be performed at any
point within the stage field limits and takes into account the stage rotation
offset.
Note: 
xT Align Feature works best at the eucentric position (see above).
Longer distances result in a greater accuracy.
Caution! 
Watch the obstacles significantly extending from the sample plane, as
these may interfere with equipment under the lens.
1. Select a long feature of interest on the sample.
2. Click the Stage menu / xT Align Feature… Choose either Horizontal
or Vertical, which relates to the desired final sample orientation. Click
the first point along the feature, the P1 coordinates update.

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 Operating Procedures: Stage Control

3. Click the second point along the feature, the P2 coordinates update.
Right-clicking anywhere in the imaging area deletes points, enabling
to define them again.

4. Drag any point to change its position, if needed. Click the Finish
button to orientate the feature either Horizontal or Vertical, as
selected previously. Click the Cancel button any time to cancel the
function.

Scan Rotation Align Feature

This procedure helps to navigate along a feature that is rotated
disadvantageously. Unlike the xT Align Feature… the rotation is
performed by scan coils instead of the stage.
1. Click the Stage menu / Scan Rotation Align Feature. Choose either
Horizontal or Vertical, which relates to the desired final sample
orientation. Click the first point along the feature, the P1 coordinates
update.

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Operating Procedures: Stage Control

2. Click the second point along the feature, the P2 coordinates update.
Right-clicking anywhere in the imaging area deletes points, enabling
to define them again.

3. Drag any point to change its position, if needed. Click the Finish
button to orientate the feature or click the Cancel button any time to
cancel the function.

Compucentric Rotation (F12)

Clicking the Stage menu / Compucentric Rotation places a green circle
in the image window. The green triangle on its perimeter denotes, by its
position, the sample rotation relative to its original position when mounted
on the stage. Initially, this is in the 12 o’clock position. Press and drag it
around the circle to choose a new sample rotation.
The readouts displayed at the image window bottom provide information
about the Actual Rotation (original position) and the Target Rotation
(the selected position).
Releasing the mouse updates the stage position to bring the original field
of view (rotated to the Target Rotation position) onscreen. With the
sample at the eucentric position this can be performed at any sample
point irrespective of the mechanical stage center.
Clicking the written angles around the circle perimeter (0° / 90° / 180° /
270°) or the perimeter anywhere drives the stage to that rotation position
and the green triangle updates onscreen. Clicking the framed + / – sign
increases / decreases the rotation angle by an incremental value.

User Units
Clicking the Stage menu / User Units activates user defined units as the
basis of the stage coordination system. A tick mark appears next to the
label and UU in the Stage module / Coordinates tab next to the X and Y
value box. The stage coordinate system reverts to the last defined user
unit configuration.
The Define User Units… procedure assigns user-defined points to stage
points. The stage coordination system can be anchored to either 1, 2 or 3
points, depending on the sample management or application.
For example, if you choose a (0,0) position, you can drive the stage
relative to that origin using user defined units (0,1 / 1,0 points), which
may equal to some repeated sample structures etc.

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 Operating Procedures: Stage Control

1. Select a sample surface feature and view it at an appropriate

magnification to check its relation to other structures.
2. Click the Stage menu / Define User Units… A Start dialogue
appears. Click the Define New User Units radio button.

Redefine User Units – for changing or updating User Units.

Redefine User Units with Shift – as above with the Beam Shift.
Reset User Units so, that they are equal to the Stage Units
Show how User Units are now defined – displays the actual
definition with the possibility to move the points step by step.
3. Click the sample user point (0,0), its coordinates appear in the
Details… module.

4. Repeat the step 3 for the sample user point (1,0).

5. Repeat the step 3 for the sample user point (0,1).

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Operating Procedures: Stage Control

6. Check the Details if needed or Finish the procedure.

Particular dialogue buttons

• Finish: ends the procedure at the point(s) 1 / 2 / 3 just defined.
• Details: displays the resulting coordinates with the possibility to
browse them (Go to button) and edit values.

Using 1-, 2- or 3- Point Alignments

TABLE 5-3 ALIGNMENT TYPE DIFFERENCES

Use 1-Point Alignment 2-Point Alignment 3-Point Alignment

Major Use Aligning to new point Aligning the stage axes with Transforming to nonstandard
directly offset from the specimen X-Y orientation units on dies or RAM arrays;
the existing location to correct for any distortion correcting for any distortion
Change in Scale None Scales the axes together X can be scaled differently from Y
Change in None Rotates both axes with a X and Y orientation can be
Orientation fixed 90° angle between axes different

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 Operating Procedures: Stage Control

Scan Rotation (Shift + F12)

This function activates the onscreen tool to rotate the scan and align the
image. Because it is solely a scan coil function, it has no effect on the
stage movements. It is used to orient the image relative to mechanical
rotation and detector direction.
Clicking the Scan menu / Scan Rotation places a green circle in the
image window. The green triangle on its perimeter denotes, by its
position, the sample rotation relative to its original position when
mounted on the stage. Initially, this is in the 12 o’clock position. Press
and drag it around the circle to choose a new sample rotation.
The readouts displayed at the image window bottom provide information
about the Actual Rotation (original position) and the Target Rotation
(the selected position).
Clicking the written angles around the circle perimeter (0° / 90° / 180° /
270°) or the perimeter anywhere drives the stage to that rotation position
and the green triangle updates onscreen. Clicking the framed + / – sign
increases / decreases the rotation angle by an incremental value.

FIGURE 5-17 SCAN ROTATION

The smaller circle in the top right of an optical quad remains onscreen
when the Scan Rotation angle is different from 0°.

Sample Navigation / Navigation Montage...

This software feature enables to navigate along the sample surface
when the field of view is smaller than desired (limited by an aperture for
instance). For this purpose it is possible to use up to 3 images which
could be changed dynamically (capture, save or load any time).
Set the Target HFW (Horizontal Field Width) range, which influences
informations fields: the tiles number – Map Size, the Estimated Time for
the procedure and the HFW of each tile – Single Image HFW.
When the Use actual HFW check box is ticked, the system does not use
automatically the HFW according to the hardware configuration and sets
the user one. This is convenient when the image corners are rounded
and imaging does not cover an entire area.
The Stage menu / Sample Navigation mode is then automatically set.
For the selected quad the upper right corner green icon indicates the
functionality.

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Operating Procedures: Stage Control

A green rectangle showing the actually selected field of view (in the
selected quad) appears with the size corresponding to the magnification.
In quad(s) using Sample Navigation the Selected Area Zooming and the
Get features could be used.
Notes: 
The basic condition for a correct functionality is an equal stage rotation
value for both captured and corresponding live images. In other case the
upper right corner red icon indicates no functionality in the respective
quad.

Navigation Alignment...
This procedure aligns Navigation image according to Reference image.

FIGURE 5-18 NAVIGATION ALIGNMENT

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 Operating Procedures: Nav-Cam (in-chamber)

Nav-Cam (in-chamber)

Helios NanoLab 450 / Helios NanoLab 450S / Helios NanoLab 450ML

On the contrary to Navigation Montage feature, which navigates across the
sample surface, this functionality represents a possibility to navigate across
a larger stage movement area, which is convenient when investigating large
area samples or several samples with the use of any multi sample holder.

CAPTURING NAVIGATION IMAGE PROCEDURE

1. Insert a sample with a LoadLock (if present) or vent the chamber,
open the chamber door, insert a sample and pump the system.
2. Select the Stage menu / Move Stage to Nav-Cam function to move
the stage to Nav-Cam position.
At this moment the beam and the detector changes to Nav-Cam and
a live imaging of navigation camera is obtained in the last time active
quad (with the resolution of 768 × 512 pixels only).
DANGER! 
Retract all retractable detectors to prevent equipment damage!
Note: 
In case you do not want to control the entire procedure, select the
Stage menu / Take Nav-Cam Photo… (Ctrl + Shift + Z) item to run
steps 2., 3. and 4. automatically at once. It is possible to cancel this
procedure by the Cancel button at any time, the stage remains in the
actual position.
3. Capture a navigation image (with the high resolution of 3072 × 2207
pixels) by using the Snapshot / Photo function. The image could be
saved or adjusted like any other image acquired from the microscope
(image enhancement, process etc.).
Note: 
Wait untill image capturing is finished (about several seconds).
4. Click the Stage menu / Move Stage to Nav-Cam function again to
move the stage to the last time stage position.
A green rectangle (or just a cross) represents a place, where electron
beam will aim.
Note: 
If the Nav-Cam observation takes longer time then 10 minutes, software
protection switches illumination off for one minute to cool down. To
proceed the operation release the quad.
Note: 
Nav-Cam usage is not possible to operate (but a navigation is still
possible) in the SEM Immersion mode (see above). 
Nav-Cam usage is restricted for highly shiny and simultaneously planar
specimens (Si wafers, mirrors etc.).
Besides a navigation image one can use also the Digital Zoom module
to navigate the stage (see Chapter 3).
When the Preferences… / General tab / Display Stage Map in
Navigation quads item is set to Yes, stage saved positions are
displayed in the Nav-Cam photo (see Chapter 3).
In case an user log off and the sample and its stage loading position did
not change, use the Stage menu / Restore Last Nav-Cam Photo.
For a dark or shiny specimens a Nav-Cam image quality could be bad. In
this case run the 401 - Nav-Cam AutoBrightness alignment (see Chapter 4).

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Operating Procedures: Loadlock

Loadlock

Helios NanoLab 450 / Helios NanoLab 450S / Helios NanoLab 450ML

The Loadlock enables a specimen exchange through the pre-pumped
Loadlock chamber, eliminating the need to vent and evacuate the entire
specimen chamber.
Note: 
It is recommended to run the Home Stage procedure each time the
specimen chamber has been opened/closed. Start the procedure after
the chamber is evacuated. 
When the Preferences… / General / Automatic Nav-Cam photo after
sample loaded option is set to yes (see Chapter 3) the Nav-Cam
navigation image (see above) is automatically acquired after sample
loading.

LOADLOCK PARTS
The Docking station
has to be mounted to enable the Loadlock use. Use two alignment pins
to position it and three screws to attach it onto the stage rotation base.
Note: 
Be careful not to drop any screw into the rotation table central hole!
Holders
Specimens stub / wafer holder is attached to the carrier, that fits into the
Loadlock arm and to the Docking station.
• The Stub Holder enables to attach six 1/2” stubs and one 1” stub in its
central hole using the inbus set screw; tighten it by a screwdriver
placed in the suitcase with holders.
• The Wafer Holder can hold large area samples. It is especially
designed to hold silicon wafers with a diameter up to 6", which can be
attached to the holder using any suitable SEM vacuum-quality
adhesive (liquid silver, carbon or double-sided tape). The specimen
must be electrically grounded to the holder to minimize its charging.

FIGURE 5-19 DOCKING STATION / 

CARRIER with STUB HOLDER INSTALLED

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 Operating Procedures: Loadlock

FIGURE 5-20 CARRIER / WAFER HOLDER / STUB HOLDER

Sample Height Gauge

Prior to a loading any sample through the Loadlock, the sample height
should be checked. The height gauge indicates the maximum height of a
sample and holder that can be loaded through the Loadlock port.
When using the carrier with the Stub holder, the specimen height is
limited to 5 mm.

FIGURE 5-21 SETTING OF SAMPLE HEIGHT

WA R N I N G ! 
The maximum specimen height can be further limited by a detector
mounted on the objective pole piece. This limitation depends on the
actual Loadlock alignment. Start the alignment 251 - Loadlock
Transfer Positions to find out the actual limits (see below).

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Operating Procedures: Loadlock

EXCHANGING SPECIMEN
Note: 
Always wear clean lint-free gloves when handling the specimen holders
or reaching into the Loadlock chamber to prevent vacuum contamination.
Note: 
Loading / Unloading sequences are enabled only when the vacuum
status is pumped (green icon).

Loading sequence
• Initial conditions: the lid is opened, the Loadlock arm is empty, both
buttons are disabled (lit is off).
1. Place the carrier on the Loadlock arm. The Clamp / Load button
becomes enabled (lit is on).
Note: 
When placing the carrier, make sure that all 3 alignment sapphires
are positioned properly.

2. Close the lid and push the Clamp / Load button. The loading
sequence starts (lit is blinking).
When the Clamp / Load button is pushed and the lid is opened, the
holder is clamped onto the Loadlock arm only. In order to continue,
close the lid and push the Clamp / Load button again, when it
becomes enabled.
• Final conditions: the carrier is in the Docking station, the Loadlock is
under vacuum, the Clamp / Load button is disabled, the Unload /
Release button is enabled.

Unloading sequence
• Initial conditions: see the Loading sequence / Final conditions.
1. Push the Unload / Release button to start the unloading sequence (lit
is blinking). After finishing, the Loadlock is vented and the lid can be
opened. Both buttons are enabled.
2. Open the lid, the Clamp / Load button becomes disabled. Push the
Unload / Release button to release the carrier from the Loadlock
arm.
3. Take the carrier out from the Loadlock arm.

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 Operating Procedures: Loadlock

LOADLOCK SOFTWARE CONTROL

Loadlock is possible to fully control from the xT Microscope Control
software via the Loadlock module, which appears on the new page after
the Loadlock installation.

Loadlock Module
Instead of pushing the hardware buttons on the Loadlock body, it is
possible to click the UI toggle buttons with the same functionality.
• Clicking the Clamp button attaches the carrier onto the Loadlock arm.
In case the vacuum status is pumped and the Loadlock lid is closed,
this action is automatically followed with the load sequence.
When the holder is clamped onto the Loadlock arm, the button label
changes to Load. Clicking it starts the load sequence (see above).
• Clicking the Unload button starts the Unload sequence. The holder is
transferred to the Loadlock chamber, which is vented lastly.
The holder remains clamped to the Loadlock arm, and the button
label changes to Release. Clicking it loosens the carrier from the
Loadlock arm.
• The State info field displays the actual Loadlock state.
• The progress bar visually indicates loading states from an Unloaded
(empty bar) to Loaded (green bar). Red progress bar indicates an
undetermined or error state (see below).

TROUBLESHOOTING
Hardware problems are indicated by a red progress bar, an Loadlock
module / State field / Indeterminate state and by the automatic
LoadLock Recovery dialogue poping-up. When closing this dialogue,
the red progress bar is replaced by the Show Recovery Dialog…
button. Clicking it opens the LoadLock Recovery dialogue again.
When the Load / Unload cycle fails due to a Touch Alarm, check the
correct specimen holder placement, the specimen size (particularly its
height) and run the Home Stage procedure before attempting another
Load / Unload action.
Note: 
When Loadlock is in any unknown state, the Load / Clamp and Unload /
Release buttons are disabled.
There are 4 types of the LoadLock Recovery dialogues corresponding to
the different error levels:
• The 1. level error indicates the software is not sure about the
Docking station state. It appears after venting / pumping the
specimen chamber or after recovering from any higher level error.
The Loadlock Recovery dialogue / Determine button moves the
stage to determine a presence of the Docking station and of the
holder.
• The 2. level error indicates a hardware error during Loadlock
inactivity.
Check the hardware, try to recover with the use of Loadlock Recovery
dialogue buttons. If it is not possible, call the service.
• The 3. level error indicates a hardware error during Loading /
Unloading sequence.
The Loadlock Recovery dialogue offers a step sequence leading to a
successful recovery. Repeat clicking the Execute Step button until
the dialogue closes.

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Operating Procedures: Loadlock

• The 4. level error indicates a hardware error which is not possible to

identify. This appears mostly during the recovering actions.
Only Supervisor or service engineer can recover from this error level.
Using the enabled buttons in the recovery dialogue with care and
according to a particular situation may lead to full recovery. Otherwise
it is necessary to call the service.

FIGURE 5-22 LOADLOCKS RECOVERY DIALOGUES

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 Operating Procedures: Multiloader

Multiloader

Helios NanoLab 450 ML

The Multiloader is a specimen exchange unit for the upgraded Flip stage.
This Flip stage contains only one site for attaching TEM samples.
TEM samples are placed on a cartridge, which is then loaded on the Flip
stage via the Transfer Gripper (displayed below with its protective cover.

FIGURE 5-23 TRANSFER GRIPPER / LIFT-OUT CARTRIDGE

After putting the sample on the cartridge (located on the Flip stage), the
sample can be unloaded from the system with help of the transfer
gripper.
Note: 
There is also equipment available to support the handling of cartridges,
TEM grids, and the transfer gripper itself. A description of this whole
process, including the different cartridges possible and a process to get
the TEM sample onto a TEM microscope, is available as a separate
(offline) user manual.

LOADING / UNLOADING GENERAL REMARKS

• During the whole process, user suggestions are displayed on the
application window.
• Canceling a started load is done by reverting the load actions.
• Canceling a started unload is done by reverting the unload actions.
• If the white LED on the multiloader base is lit, the multiloader base is
in an error state and service is needed to repair the multiloader base.
• A multiloader (un)load is only possible in a pumped state.

Loading Cartridge
1. Place the transfer gripper (loaded with a cartridge) in the multiloader
base.
2. Press the LOAD button and wait until the button stops blinking.
The stage of the microscope moves to the position at which the
transfer of the cartridge from the transfer gripper to the Flip stage can
take place. This takes awhile, so wait for a message in the application
window to indicate the movement is complete.

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Operating Procedures: Multiloader

3. Rotate the transfer gripper counterclockwise and let it slide into the
microscope.
4. Rotate the transfer gripper clockwise and let it slide out of the
microscope.
5. Rotate the transfer gripper clockwise.

The transfer gripper is now locked in the multiloader base, until a

successful load is done.
The cartridge is loaded and the system is ready for normal use.

Unloading Cartridge
1. Press the UNLOAD button and wait until the button stops blinking. In
this time period, the stage of the microscope moves to the position at
which the transfer of the cartridge from the Flip stage to the transfer
gripper can take place.
2. Rotate the transfer gripper counterclockwise and let it slide into the
microscope.

3. Rotate the transfer gripper counterclockwise and let it slide out of the
microscope.
4. Rotate the transfer gripper clockwise.

5. Pull the transfer gripper backwards to remove it from the microscope.

The cartridge is unloaded and the system is ready for normal use.

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 Operating Procedures: Measurement and Annotation Functions

Measurement and Annotation Functions

The Processing page / Measurement / Annotation functions give an

user many capabilities to measure distances, angles, diameters and
areas as well as locating and labelling items that are of significant
interest on the sample area.

TOOLS
Selected measurement or annotation tool is displayed as the tool icon.
Clicking the icon activates / deactivates the tool (the active one is
highlighted). Clicking the arrow next the icon symbol opens the list of
available tools to choose. The appropriate icon is shown from that time
on and the item can be drawn on screen. The drawn items are listed in
the list box.
• The Measurements enable to gain dimension information about a
specimen feature by overlaying it with a measurement graphic. By
changing the magnification these graphic elements resize
accordingly.

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

• The Annotations enable to graphically label items of interest.

• The Text enables to add further information.
• The Trash can button deletes selected item(s).




The Measurement / Intensity Profile delineates the imaging profile

across a freely selected line with a set of properties.

Property Editor
enables to change a lot of properties of a selected Measurement /
Annotation / Text graphic by selecting from the drop down list or by a
direct editing of a text or a value. Each graphical element has its own set
of appropriate properties.

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Operating Procedures: Measurement and Annotation Functions

Shape Creating
1. Choose the suitable Measurement / Annotation graphic tool.
2. Draw the graphic over the area of interest. This can be done by:
– pressing and dragging the cursor from the top left corner to the right
lower corner of the shape.
– SHIFT + pressing and dragging: the shape starts to grow from the
point where you have clicked as from the center.
3. Choose the Text symbol and then just click where you require a text
in the image. Type the text into the Property editor text field. Click the
text or press the enter key to confirm it and the text appears
onscreen.

Shape Editing
Once a Measurement or Annotation symbol has been drawn, it can be
modified. Selected graphic is denoted by the addition of resizing
handles to the graphic outline (use pointer cursor).
Size and position the graphic correctly over the area of interest.
A number of other choices are available in the Property editor for each
graphics drawn.
• Move / Rotate graphic: press the cursor inside the boundary of the
pattern / in the vicinity of a corner and drag it (move / rotate cursor).
Pressing the Ctrl + Alt keys while hitting any arrow key moves the
pattern in an arrow direction for a fixed distance.
• Resize graphic: press and drag the resizing handle until the desired
size is reached (horizontal / vertical / diagonal resizing cursor).
Pressing the Ctrl key while dragging forces dimensions to be changed
proportionally. Precise dimensions could be also entered in the
Property editor.
• Selecting all Items (in an selected quad): press Ctrl + A.
• Delete selected Item(s): click the Trash can icon or press the
Delete key.

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 Operating Procedures: Patterning

Patterning

Patterning is the process of moving a beam over the defined pattern

along the specimen surface (while leaving other areas untouched) with
the purpose of:
• the milling – removing well-defined amounts of existing material 
(the pattern is displayed in yellow color),
• the deposition of well-defined amounts of new material (the pattern
is displayed in color appropriate to the GAS selected - see below).
The electron beam is generally used for deposition while the ion beam
for both processes.
The Pattern module (see below) and the Patterning menu (see 
Chapter 3) controls the entire proces.
Caution: 
When patterning or milling a large volume of material at higher ion
currents, it is recommended to remove any detector (both lens mounted
and retractable one) if it is not used. There is a risk of its efficiency
decrease by a material deposition.
The system provides additional monitoring possibilities:
• the Simultaneous Patterning and Imaging (SPI)
The SPI provides an electron imaging (in different quad from patterning)
during patterning. It is strongly influenced by secondary electrons
generated by the ion beam (SE imaging). The higher electron currents
(higher spot numbers) and averaging help to improve the imaging. In
case the BSE detector is used this interference is less important (BSE
imaging). The system remembers the brightness and contrast setting for
each modes (SPI or normal imaging).
• the Integrated Real Time Monitor (RTM)
The RTM provides an immediate imaging (in the same quad with
patterning) of the patterning process. The patterned area is observed and
in case of relatively slow scanning, the scan trajectory can be inspected.
RTM is typically used as an end pointing device by observing brightness
differences in the detector signal. These result from contrast differences
(when milling through layers of different composition on a stack of
multiple materials or releasing a TEM foil from the Omniprobe tip).
RTM can be used with electron or ion beam and with any of the pattern
types that are available in the UI. When starting patterning with the RTM
activated, the pattern in the UI will be updated with real time image
information. The patterned area information is updated based on the
detector signal which is displayed in synchronization with the beam
trajectory.
Because the detector signal is synchronized with the scan of the
patterning beam (usually FIB), the other beam cannot be used to make a
live imaging while patterning. As an alternative, it is of course possible to
grab snapshot with the electron beam during FIB patterning while using
RTM.
Note: 
The acquired data are matched to the calculated positions of the
corresponding milling points, the pixels shown on the screen may not
therefore directly match to what is happening on the sample surface and
some imaging artifacts (due to milling points and screen pixels
mismatch) could occur. To prevent this try to change the field of view.

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Operating Procedures: Patterning

PATTERN MODULE
There are several tool icons, Basic / Advanced / Progress / S. Mill tabs
and the Progress monitoring area within the module.












Tool Icons
Clicking the icon activates (highlighted with an yellow background) /
deactivates (normal backgroud) the tool. If no icon is selected, the
pattern selection cursor (arrow) is active.
• The Pattern type selector: Clicking the arrow next to the icon
activates the drop down list to select a pattern type (see below): 
Rectangle / Cleaning Cross Section / Regular Cross Section /
Circle / Line / Polygon / Bitmap / Stream File.
• The Trash Can (Delete) button deletes the selected pattern(s).




• The Pattern / Exclusion Zone (overlapping area of the two patterns)

Enable / Disabled button sets selected pattern / exclusion zone to be
/ not to be processed.
• The Hide / Show button hides all patterns in the selected quad.
• The Patterning Serial / Parallel sequence button switches between
two possibilities (see below).
• The Zoom button enlarges selected pattern / patterns to fill entire
quad.







• The Patterning sequence buttons set the process order.

Patterns are milled in the order they are created. Numbers are
displayed close to the pattern and in front of its name to indicate the
actual milling order. This can be changed by clicking the left / right
single arrow to move the selected pattern one position up / down and
by clicking the left / right double arrow to move it to the first / last
position.

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 Operating Procedures: Patterning

Pattern Types
Patterns are automatically assigned to one or more particular processes.
They are distinguishable by a different cross-hatch.
The Rectangle pattern is dedicated to both milling and deposition.
The Cleaning Cross Section pattern is processed line by line 
(each line with set number of passes).
The Regular Cross Section pattern has two possibilities selectable in
the property editor (see below):
• Scan Method: Multipass – processes entire pattern and starts again
(with set number of passes).
• Scan Method: Stairstep – the pattern is created as a compilation of
five rectangles with specified overlap between them. Each one is
processed with the set number of passes.
The Bitmap pattern enables to import bitmaps as a pattern. In this 24
bits RGB bitmap each pixel consists of:
• the Red component – actually not used,
• the Green component – determines if the beam is blanked. Any other
value then 0 activates the beam,
• the Blue component – determines the dwell time per pixel. If the
value is 0 no milling or deposition proceeds, if it is 255 the maximum
dwell time is used. The dwell time for values in between is linearly
interpolated and then assigned to a value from the table (124 entries
from 100 ns to 4,6 ms) with respect to the actual value set within the UI.
Note: 
When drawing a bitmap it is recommended to use black (0 / 0 / 0) for
none milling points and white (255 / 255 / 255) for milling points. 
Do not forget to optimize other properties such as application file (see
below), depth, leading edge etc.
The Stream File pattern is created as an ASCII text or binary file that
addresses directly the patterning DAC (Digital Analog Converter) and
produces custom pattern files. The 16-bit DAC is used so the patterning
field is divided into 65 536 steps in both X- and Y- axis, but imaging is
restricted to only 12-bit which represents 4096 steps.
s 96 2867 2867 96 1639 2048 96 2457 1639
40  96 1229 2457 96 2048 2048 96 2867 1639
25 96 1639 2457 96 2457 2048 96 1229 1229
96 1229 2867 96 2048 2457 96 2867 2048 96 1639 1229
96 1639 2867 96 2457 2457 96 1229 1639 96 2048 1229
96 2048 2867 96 2867 2457 96 1639 1639 96 2457 1229
96 2457 2867 96 1229 2048 96 2048 1639 96 2867 1229
The file must begin with an s, indicating a stream file. The second line
defines the number of loop repeats (40 times). The third line indicates
the total number of X, Y coordinates (pixels) in one loop (5 × 5 = 25 in
this case). The 96 figure represents dwell time in units of 0.1 µs (9.6 µs).
The range of dwell time is 0.1 µs to 4.6 ms, with 124 values distributed
approximately logarithmically within this range.
Note: 
Stream files cannot be created directly from xT UI, use any suitable text
processor. There are several stream file types, which are recognizable
by the first header line (s16 / s16,25ns / s16,DAC / s16,25ns,DAC).
When two patterns are overlapping, it is possible to join them into one
pattern by use of the Build Polygon functionality.
Selected patterns could be multiplied by the use of Build Array
functionality. The Dimension / Pitch means number of repetition / distance.

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Operating Procedures: Patterning

Serial Patterning
All patterns defined on the screen are processed consecutively; 
milling / deposition is completed on one pattern before moving to the
next one. Serial patterning is always used with cleaning cross section
milling. This is the default patterning mode.
Parallel Patterning
All patterns defined on the screen are processed concurrently, 
one pass of the beam is completed on all patterns before moving to the
second pass. Parallel patterning is typically used with regular cross section
milling and to avoid a redeposition of material on the adjacent areas.
With parallel patterning, the mill time is recalculated to include all the
patterns that are displayed in the image window.
When an user changes to the Parallel mode, the following pattern
properties in the group must necessarily be the same: Number of
Passes, Beam, and Gas properties. The first selected pattern determines
these values for all other ones.
Other properties (Application File, Overlap, Sputter Rate, Recovery Time
and Depth) are also all set to those of the first selected pattern to avoid
confusion, even though they could theoretically remain unchanged.
Restoring Serial mode does not undo these changes; the properties
remain as in the Parallel mode.
Patterns Processing
Select the pattern from the Pattern type selector drop down list. Once
selected, the cursor is ready to draw a suitable pattern onscreen (quad or
single screen).
• Importing / Exporting Patterns
Defined patterns may be imported via the File / Import / Patterns… menu
item or exported (saved) via menu File / Export / Patterns… menu item
(see Chapter 3).
The saved file (.ptf) contains all parameters found at the Patterning
property editor (Basic / Advanced - see below) for all patterns drawn in
the selected quad. It could be assigned to one of six (A - F) toolbar
Pattern Preset buttons (available only if activated via the Preferences…
/ General tab) by right-clicking above the selected button (becomes
yellow):
The Apply starts the patterning with the preset parameters 
(the same as clicking the button directly).
The Edit… opens the Pattern File (.ptf) selection process.
The set of toolbar Pattern Preset buttons could be saved / loaded by the
File / Export / Import / System Parameters… menu (see Chapter 3).
• Pattern Editing
Once a pattern shape has been drawn, it can be modified.
Selected Pattern is denoted by the addition of resizing handles to the
pattern outline (pointer cursor).
Move / Rotate Pattern: press the cursor inside the boundary of the
pattern / in the vicinity of a corner and drag it (move / rotate cursor).
Holding the Ctrl + Alt keys while hitting any arrow key moves a pattern in
a respective direction for a fixed distance (one screen pixel).
Resize Patterns: press and drag the resizing handle until the desired size
is reached (horizontal / vertical / diagonal resizing cursor). Pressing the
Ctrl key while dragging forces dimensions to be changed proportionally.
Precise dimensions could be also entered in the Property editor.

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 Operating Procedures: Patterning

Select all Patterns (in an selected quad): press Ctrl + A keys or click
the Select All button.
Delete selected Pattern(s): click the Trashcan icon or press the Delete
key.

Basic and Advanced tabs

A certain pattern could be selected by the list box with many associated
parameters which could be set via the patterning property editor:
• The Application: Clicking the value slot produces a drop down arrow
bringing a list of applications. Choosing the required one sets the
subsequent properties.
• The X / Y / Z size: dimensions of the pattern
• The Scan Direction (Bottom To Top / Top To Bottom)
• The Dwell Time: a time the beam spends on a single pixel per pass.
• The Beam to be used.
• The Time required to process this pattern
• The Position X / Y of the pattern relative to the origin (the quad
center).
• The Rotation of the patterns (the positive direction is clockwise).
• The Gas Type: The gas to be used to process the pattern (or None if
no gas is to be used). This determines the pattern color onscreen.
• The OverlapX / Y sets the beam diameter overlap. The value of the
overlap can be positive or negative depending on a particular
application. The overlap parameter influences the Area Calculation
and the Dose.
• The PitchX / Y sets the pitch between two spots.
• The Area Calcualtion defines how the patterning area will be
calculated in order to get the most accurate value of the Dose. This
value is related with the OverlapX/Y. The Pattern (default) / Array are
set for positive / negative overlaps.
• The Dose defines charge dose per area. Be aware of different values
depending on Area Calcualtion setting.
• The Vol per Dose: The volume of material that is removed per
charge.
• The Sat Sput Rate: The maximum linear sputter rate for a given gas.
For Gas = None this is 0 (actually not used).
• The Refresh Time: The minimum loop time that must at least elapse
before the next pass, so that the adsorbed gas can be refreshed.
• The Loop Time: The time required for a single pass (read only).
• The Area: The surface area of the pattern (read only).
• The ScanType: the Serpentine means the beam proceeds from left
to right and back from right to left, while the Raster scans from left to
right, then the beam is blanked and returns to the left starting point.
• The Fill Style: one can choose either to mill a solid or just a frame
(box and circular types only).
• The number of Passes that the beam scans over the pattern
• The Defocus of the beam (WD change) - influences the Total
Diameter and Area Calculation. It allows focusing above / below
(negative / positive value) the sample surface.
• The Blur: Like Defocus, but specifying the (additional) diameter of the
blurred spot.
• The Interaction D for an infinitely small beam - influences the Total
diameter.

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Operating Procedures: Patterning

• The Total Diameter: The combination of the beam diameter and

interaction diameter - influences the OverlapX/Y and PitchX/Y values
(read only).
• The Max dose p A describes the adsorbed gas layer, allowing a
certain dose to be deposited at a higher rate than the saturation
current density, allowing a temporary higher rate (actually not used).
• The Sat cur dens: The current at which 63% of the saturation sputter
rate is reached (actually not used).
• The Tot V sput r: The speed at which material is removed or
deposited (actually not used).
• The Selective Milling Enabled / the Selective Milling Time Interval
/ the Min Contrast Treshold / the Max Contrast Treshold items
corresponds to the Selective Mill Tab elements (see below): Enabled
check box / Interval adjuster / left and right borders of the grey leve to
be processed for the selected pattern.

Progress Tab
Here one can observe patterning progress and check some milling
properties.
• Time Elapsed: elapsed patterning time
• Time Remaining: estimated remaining patterning time
• Time Total: estimated total patterning time
• Accumulated dose: total dose from the start of patterning
• Accumulated depth: entire milled depth of all processed patterns.
• Chamber Pressure displays actual chamber pressure.
• The Acquisition Delay continuous adjuster corrects defect imaging
during patterning. Use 0 s when not sure.

Selective Mill Tab

It is possible to set a given grey level to be processed in the extent of the
selected pattern area.
• The Scan button reads the pattern area grey level histogram.
Move the vertical black line to a desired grey level position and also
move the red rectangle edges to set the grey level extent.
• When the Enable check box is ticked the selective milling is enabled.
• The Interval continuous adjuster sets the time [s] after which the
histogram is actualised.

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 Operating Procedures: Patterning

PROGRESS AREA
Information updated as the milling progresses are found here (captions
change according to a running process):
• the Total / Remaining Time: estimated total / remaining patterning time
• the Overall Progress – related to the total patterning time of all patterns
• the Current Progress / CCS Line Progress – related to the actual
pattern in progress
• skip to a next pattern in order
• Skip to a next line (available only with Cleaning Cross Section)
• Skip to a previous line (available only with Cleaning Cross Section)
• The Select All button selects all patterns in the active quad.
Note: 
When patterning is paused in one quad it is possible to start patterning in
another one. Similarly when patterning finishes there may still be a
paused pattern in another quad.
It is possible to acquire an image from the signals generated during
patterning. All imaging parameters are dictated by the patterning
requirements and only the areas visited by the beam during patterning
are recorded. Much better images can be recorded by a Snapshot during
patterning. In this case patterning is paused, an image is recorded and
patterning resumes.
Note: 
If the magnification is too high, creating certain patterns can use too
much memory needed for the control system to run. The pattern corners
become round and the edges become jagged. A good rule of thumb is to
pick a magnification where your pattern fills 35-50% of the screen.

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Operating Procedures: Patterning

END POINT MONITOR (EPM) MODULE

The EPM gives visual feedback on the progress of a milling process. It
displays the charge absorbed in the specimen (specimen current) and
enables to monitor the specimen current changes as the ion beam
interacts with different materials in the sample. For example the
differences encountered when milling through some dielectric and
striking another one are usually very subtle, but once the beam begins
milling into metal, a dramatic difference in absorbed charge could be
observed on the EPM graph.

iSPI Tab 
(intermittent Switching between Patterning and Imaging)
• Ticking the On check box starts the iSPI mode, in which the ion beam
is paused during electron imaging to minimize the interferences.
The graph of milling progress starts automatically to draw when
patterning starts. When patterning is paused or stopped / resumed it
stops / continues drawing the graph.
• The Pause check box pauses the electron quad after image
acquiring.
• Ticking the Save check box saves all electron images grabbed during
the process.
• The Time Interval slider sets the interval after which the system
acquires an electron image and pauses the electron imaging.
• The CCS Line Interval slider sets the number of lines after which the
system acquires an electron image and pauses the electron imaging.
For a Cleaning Cross Section, select a CCS Line Interval to take an
electron beam image every “×” number of slices. For all other
patterns, select a Time Interval to take an electron beam image every
“×” number of seconds.

Monitor Tab
illustrates the milling progress as a colored graphical display, showing
the accuracy for depth or material changes over the whole milled area.
Graphs can be saved by the File menu / Export / End-Point Monitor
Graphs or loaded by the / File menu / Import / End-Point Monitor
Graphs. All existing graphs are saved, loading adds saved graphs at the
end of the list of graphs; it does not clear or overwrite existing ones. In
case of name conflicts the loaded graph is renamed.
Clicking the green rectangle in the upper module corner provokes /
hides a large graph window. It depicts:
• yellow line (right Y-scale) – Stage (specimen) current (see below)
• other colored lines (left Y-scale) – Grey Scale (RTM data) from
patterned area (see below)
When serial patterning mode is set, there is only one graph, when
parallel one is set, there could be more of them.
• The X-axis menu (Dose Accumulated / Depth Penetrated / Time
Elapsed) offers the choice for X-axis description.
• In the Browse menu (First / Previous / Current / Next / Last) 
one can list in all graphs stored (see Browse section icons).

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 Operating Procedures: Patterning

• In the Navigate menu it is possible to handle the selected graph 

(see Navigate section icons):
- Zoom (scale) In / Out 
- Pan (move graph to the desired position)
- Reset to default values
- Measure line points positions (see values on the left side).

Notes:
Each time patterning is started the EPM automatically adds a new graph
(if the EPM is switched on). Resuming patterning continues the graph
that was created when patterning was started.
Initially the graph is Auto-Scale, meaning that the minimum and
maximum of both axes are computed automatically so that all the graphs
are completely visible. As points are added during patterning the graph
may rescale to achieve this.
Dragging a rectangle in the graph when in Zoom In mode zooms in that
rectangle and the graph switches to fixed-zoom. Switching back to Auto-
zoom is possible via the Navigate menu / Reset item.
When the graph is zoomed-in a user can click & dragg the graph in the
Pan mode.
Graphs can be selected by clicking any one; the selected graph is
indicated by several black selection rectangles. Clicking outside any
graph deselects all graphs. New graphs are selected by default so that
the Options tab displays their properties. It is not possible to select
multiple graphs.

The Settings Tab

• Plot Mode / Auto-Scale sets graph magnification according to
X Scale % value.
• Plot Mode / Auto-pan moves present milling position in the graph
window according to Auto Pan % value.
• The SE (Secondary electrons) check box: switches visibility of RTM
curve on / off in Monitor graph.
• The Stage Current check box: switches visibility of stage (speciment)
current curve on / off in Monitor graph.
• The Reset button resets values to default.
• The Apply button propagates new values.

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Operating Procedures: Patterning

GAS INJECTION MODULE (OPTION)

Patterns have many associated parameters, such as the gas that can
optionally be used during patterning to increase the speed of the process
and which is deliverred by a Gas Injection System (GIS).
As different applications require different gases, there could be more
GIS’s installed on your system. One can select an Application file for a
given pattern in Patterning property editor. It automatically sets the
appropriate GIS, the dwell and overlap, calculates the proper dose
appropriate to the beam chemistry. A pattern type must be defined
before an application file is selected.
The GIS can be selected manually, but note that overlap, dwell and an
appropriate gas type should be set carefully to avoid disappointing results.

Setting up the GIS

The Gas Injection module enables to control installed GIS’s. A Gas
Type is allocated to each GIS (up to 5 injectors may be mounted on the
system in total). A tool tip info is given about the selected GIS line:
• Port: Port # – GIS connection position
• Lifetime: a time of GIS employment
Before the patterning with the GIS starts, the GIS needle must be
inserted manually and the gas reservoir must be heated. The GIS valves
opening / closing is automatic during patterning.
Double-clicking or the right clicking over the installed GIS module line
opens a dialog list. By clicking the Heater selection the Heat / Cold
status is replaced by a progress bar, which in turn is replaced by the
Heat / Warm status when the GIS is fully heated.
Clicking the In box (its color depends on the Gas Type) enables to insert
(tick mark) / retract (clear box) the GIS. A confirmation dialog appears.
Note: 
Confirm the insertion if you know there is nothing obstructing its travel.
Caution! 
Beware of stage moves while GIS is inserted! The GIS needle could be
damaged by incautious stage movements!
Some conditions must be fulfilled before the insertion is enabled, which
is notified by a tool tip.
To open / close the GIS valve double click the Closed / Opened status in
the Flow column. It will not be possible to open the valve if the GIS
heater is not in Warm status.
Note: 
If a gas type in patterning property list is chosen, the opening / closing of
GIS valves is done automatically during patterning.
When not in use, the GIS should be closed (to save lifetime), cold and
retracted. Leaving it closed, heated but retracted is also an option so that
reheating is not necessary if it is to be used over several patterns.
Caution! 
Logging off an actual user does not change conditions of GIS’s. 
It could be Warm, In and Opened even if the xT microscope control
software is closed!
Caution! 
When the vacuum status is vented, GIS needles are retracted
automatically. In spite of that retract it/them manually before you start any
activity inside the chamber (specimen exchange, detector mounting etc.).

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 Operating Procedures: Patterning

APPLICATION FILES
There are several application files delivered with the system which are
intended for different use. Each one incorporates multiple parameters for
particular patterning. Some of these application files use GIS’s. With
multiple GIS’s installed on your system you can select a suitable application
file for a given pattern. Processing specific materials without gas can be
done by using no application file, or more efficiently with the appropriate
scanning conditions using the dedicated Application file for that material.
There are pre-defined (non-editable) and user-defined (saved) files.
Note: 
A pattern must be defined before the Application file is selected, the
pattern type automatically predetermines the set of possible application
files (therefore a gas type).
Note: 
Within the application files compilation there are former Si application file
with Volume per Dose value determined in the past and the Si-New
application file with values corrected for use with the silicon. Be aware
about different results using these application files!

Application Files Editing

New application file can be created or an actual Application file can be
edited in the Windows Notepad® in case any parameter of the process is
insufficient. xT Application files (*.xml extension) are located in the 
C:\Program Files\Fei\data\patterning application files\ directory.
Note: 
If any Application file is to be changed it is recommended to make a copy
of the original one. Server restart is necessary after placing a new
Application file to the above mentioned directory to be functional.
Examples
For clear arrangement there are comment lines within an xml files:
• the comment line filter
<!-- Application file for milling silicon (Si) without any gas -->
In order to make the application files selection more comprehensible
several filters has been implemented:
• the beam type filter
The system only displays application files which are related to a beam
type set (if an ion beam pattern type is selected, application files
which have it designated are displayed).
<Beam xmlns:dt="urn:schemas-microsoft-com:datatypes"
dt:dt="string">Ion</Beam>
This setting filters out all application files related to the electron beam.
If the command is left blank the file is displayed for both beams.
Note: 
The I in ion or E in electron must be capitalized.
• the pattern type filter
The system only displays application files which are related to a given
pattern type.
<!-- Optional type, must be "Line, Circle, Rectangle, RCS, Bitmap,
StreamFile, Polygon", can be a combination -->
<PatternType xmlns:dt="urn:schemas-microsoft-
com:datatypes"dt:dt="string"> CCS</PatternType>
Multiple patterns can be designated in a list separated by comas. If
the command is left blank the file is displayed for all pattern types.

CONFIDENTIAL FEI Limited Rights Data 5-65

Operating Procedures: Patterning

• the GIS type filter

The system only displays application files depending on GIS’s
installed on the system.
It is possible to edit / add / remove parameters (for instance Refresh
Time - for filling vias, Blur - for depositing large areas etc.) if required for
certain applications.
• the Volume per Dose variable can be edit at:
<VolumePerDose xmlns:dt="urn:schemas-microsoft-com:datatypes"
dt:dt="r8">
0.15e-9
</VolumePerDose>
The Volume per Dose is material dependent. Using any application
file for milling different material substrates results in a differnet Z size.
The actual value can be measured and subsequently a new Volume
per Dose value can be defined / set.
When using the ion beam (without any gas environment at 30 kV) the
Volume per Dose values (Sputter Rates) for various materials can be
found in the following table.

TABLE 5-4 MATERIAL SPUTTER RATES AT 30 kV

Volume per Dose Volume per Dose

Material [µm3 / nC] Material [µm3 / nC]
C 0.18 Au 1.50

Si 0.27 MgO 0.15

Al 0.30 SiO2 0.24

Ti 0.37 Al2O3 0.08

Cr 0.10 TiO 0.15

Fe 0.29 Si3N4 0.20

Ni 0.14 TiN 0.15

Cu 0.25 Fe2O3 0.25

Mo 0.12 GaAs 0.61

Ta 0.32 Pt 0.23

W 0.12 PMMA 0.40

Note: 
PMMA - PolyMethylMetaAcrylat

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 Operating Procedures: Patterning

Application Files Examples

The non-gas assisted milling: the Si new application file:
• Beam Type: Ion
• Dwell Time: 1.0 e-6 s
(The time the beam spends on a single pixel per pass.)
• Overlap: 50% (Sets the beam diameter overlap.)
• Volume per Dose: 0.27 e-9 m3/s
(Describes the amount of material volume removed per charge. This
is called sputter rate in previous dual beam tools.)
The gas-assisted application file: the Tungsten application file:
• Beam Type: Ion
• Dwell Time: 250 e-9 s
(The time the beam spends on a single pixel per pass.)
• Overlap: - 50% (Sets the beam diameter overlap.)
• Volume per Dose: 0.025 e-6m3/nC
(Describes the amount of material volume removed per charge. This
is called sputter rate in previous dual beam tools.)
• Refresh Time: 0 (Adds the waiting time between each pattern pass.)
• Blur: 0 (Defocus the beam to increase deposition for large areas.)
If the overlap is positive the mill time can be calculated based on the
volume per dose parameter and the beam current:

For example, create a filled box pattern (5 × 5 × 2) µm (X × Y × Z, the

desired material volume to be milled: 50 µm3) and choose 0.5 nA, which
is 0.5 nC/s. Therefore:

Doubling the Z size , the desired volume would be twice larger and the
milling time twice longer, doubling the beam current cuts milling time in
half.

CONFIDENTIAL FEI Limited Rights Data 5-67

Operating Procedures: Plasma Cleaner

Plasma Cleaner

Model difference: 
Option for Helios NanoLab 600i.
The Tools menu / Sample Cleaning… item starts the Sample Cleaning
procedure, which is an efficient process for removing very thin
contamination layers, which are typically formed by hydrocarbons
residues remaining on vacuum parts after conventional cleaning or could
be transferred into the microscope chamber with a sample.
The plasma cleaner generates free oxygen radicals, which react with
hydrocarbon molecules on the surfaces to form CO, CO2, and H2O
molecules that can be pumped away. It is operated at vacuum conditions
similar to the low vacuum operation (~50 Pa).

FIGURE 5-24 PLASMA CLEANER

The Sample Cleaning procedure uses cleaning times up to 5 min, which

is possible to set in the 104 - Plasma Cleaning Alignment (see below).
For avoiding of typical “weak” contamination artefacts during high
resolution imaging (image darkening), 1-2 minutes plasma cleaning
duration in combination with cryo cleaning (see above) should be
sufficient. When bulky deposition is visible (mostly on image corners),
5 minutes duration is recommended.
Note: 
Porous, biological or hydrocarbon based samples cannot typically be
viewed without presence of contamination artefacts even after plasma
cleaning, which is caused by presence of contamination source in the
sample itself. 
Sometimes, poor image quality could be caused by e-beam etching and
re-deposition of etched material also.

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 Operating Procedures: Plasma Cleaner

SAMPLE CLEANING PROCEDURE

1. Move the stage to the lowest Z-axis position.
2. Run the Tools menu / Sample Cleaning… procedure.
It is possible to enter the procedure from the vented state with the use
of Vacuum or Load Lock module also. When the procedure is
finished or aborted by an user, the system remains evacuated.
During the procedure run, stage moves are disabled temporarily.
3. Move stage back to the observation position.
When starting the procedure and some conditions are not allowed, the
dialog or tooltip appears onscreen.
Warning! 
If EDS / WDS / EBSD system is mounted, use 1 mm collimator on EDS
detector and do not exceed 5 minutes overall procedure duration once a
day at most. 
Always retract EDS detector before plasma cleaning! 
Avoid leaving sensitive carbon containing samples (e.g. photo resist)
inside the chamber during Plasma Cleaning procedure, as they may be
etched by the cleaning process. 
Any material that can create or release oxide easily (e.g. silver) should
not be plasma cleaned (Au-C resolution tests samples could be left
inside the chamber during the Sample Cleaning procedure).

CONFIDENTIAL FEI Limited Rights Data 5-69

Operating Procedures: Plasma Cleaner

5-70 FEI Limited Rights Data CONFIDENTIAL

6 MAINTENANCE

This section describes necessary microscope maintenance procedures

that can be carried out by the FEI Supervisor User / FEI Microscope
User. The user maintenance is at a minimum due to gun and column
design providing the long uptime. Therefore a complicated maintenance
is normally a part of a service contract to be performed by a qualified
service engineer.
At the User level items such as the following can be maintained:
• Cleaning Procedures Overview
• Stage Maintenance

Caution! 
- Parts that operate in vacuum should be handled carefully using clean
powder-free gloves. Parts not in use should be stored in suitable
containers or packed in aluminium foil. 
- the EDX window (option) is very fragile and must be protected from
large pressure oscillations. It is also recommended to remove the
detector before major cleaning activities. 
- Be aware of removing the chamber door locking screw(s), used during
an instrument transportation (labeled REMOVE)! If these are installed,
an overpressure over 20 kPa (150 Torr, 0.2 bar) can arise inside the
chamber during the vent procedure (N2), which is harmfull to the EDX
window, if installed.
Note: 
Gas back fill (N2) should be maintained while the specimen chamber is
at ambient pressure. However, to avoid gas waste it is recommended the
chamber should be left vented no longer than necessary.

CONFIDENTIAL FEI Limited Rights Data 6-1

Maintenance: Cleaning Procedures Overview

Cleaning Procedures Overview

Frequency of cleaning is, in most cases, determined by necessity due to

poor image quality or gross astigmatism level. Recommended cleaning
procedures are given below for parts which operate in vacuum and which
are subject to possible contamination.

LIST OF APPLIED CLEANERS

• De-ionized or distilled water – H2O
• Ethanol – C2H5OH
• Ethanol p/a (Pro Analysis: 99.8% pure) – C2H5OH
• Isopropanol
• Neutral pH cleaning fluid (soap solution)
• CIF* or SOFT SCRUB (fine abrasive household cleaner) 
or 0.05 µm aluminous powder
TABLE 6-1 HOUSEHOLD CLEANERS

Country Name
Austria CIF
Australia CIF
Finland CIF
France CIF
Germany CIF
Italy CIF
Japan CIF
Netherlands CIF
Switzerland CIF
UK CIF
USA Soft Scrub

WARNING! 
The cleaning solvents ethanol and isopropanol are highly flammable! Do
not use open flames and do not smoke while cleaning. Ventilate the
room properly.

CLEANING COLUMN PARTS

All column parts are polished before the instrument is delivered. For this
reason only occasional light polishing is required to remove
contamination that may build up on components in the specimen
chamber as part of normal operation. Any part that is exposed to the
electron beam should be highly polished, and free of contamination and /
or scratches that can charge and thus degrade the image.

6-2 FEI Limited Rights Data CONFIDENTIAL

 Maintenance: Cleaning Procedures Overview

Caution! 
Gold plated parts should not be polished with abrasive.

MATERIALS AND TECHNIQUE

To polish components, place a lint-free cloth on a flat surface (a glass
block is ideal) and apply a small amount of Soft Scrub or CIF and distilled
water to the cloth.
Place the part to be cleaned on the polish and rub with a circular motion
until all contamination has been removed. For inner surfaces, use a
cotton swab or wooden dowel as an applicator. A toothpick can be used
for small holes.
Lint-free nylon (not cotton) or latex surgical gloves should be worn while
handling parts to avoid contaminating just-cleaned surfaces. Tweezers
should be used to hold small parts.
After the part has been polished, remove the Soft Scrub/CIF cleaner by
washing in hot water. Inspect the part under a stereo microscope at 20×
magnification to ensure that there is no remaining contamination or
polish residue. Wash the part in de-ionized or distilled water in a beaker
with an ultrasonic cleaner for several minutes.Transfer the part to a clean
beaker with alcohol or isopropanol and clean ultrasonically again for
several minutes.
When the components are dry (a compressed air ‘duster’ can speed
drying), reassemble and return to the column. If a part is stained, heat it
with hot water and immediately rinse with alcohol and dry using
compressed air.

Cleaning Tips
Parts exposed to the electron beam require periodic polishing. This will
ensure maximum performance of the instrument for many years.
Do not use metal polishes such as POL or WENOL to clean parts as
these can leave outgassing material. Be aware that threaded surfaces
should not be polished as these do not have contact to the beam and are
a source of outgassing if polish is trapped. Wash threads with alcohol or
isopropanol if absolutely necessary.
After cleaning, inspect all parts for residue and stains using a light
microscope.

CONFIDENTIAL FEI Limited Rights Data 6-3

Maintenance: Stage maintenance

Stage maintenance

STAGE MECHANICS
Checking the condition of the stage should be a weekly exercise as
many different samples may be exchanged in this time period. Some
samples may be powders or composite materials that inadvertently drop
particles on or in the stage. If a silicon wafer breaks in the chamber it can
shatter into hundreds of pieces. In this case the stage should be
thoroughly cleaned before attempting movement again.

Cleaning Stage parts

Abrasive and solvents must not be used on the moving stage parts.
Cleaning by a suction is the ideal method. If not available, cleaning
should be done by using dry nitrogen gas bursts around the stage
mechanics to blow out any foreign materials. Make sure the final lens
and detectors are protected from the turbulence. Do not use sharp metal
objects to scrape away debris. A fine pair of plastic tweezers can be
used to pick up difficult particles. Spillage on the stage should be wiped
up using a lint-free cloth, followed by suction or blowing with clean
gaseous nitrogen.

SPECIMEN HOLDERS
Recommended cleaning procedures are given below for parts which
operate in vacuum and which are subject to possible contamination.
Frequency of cleaning is, in most cases, determined by necessity (image
quality or astigmatism level).

Cleaning
1. Clean these parts using a lint free cloth and a mild abrasive domestic
cleaner (see above).
2. Rinse in tap water.
3. Clean in an ultrasonic cleaner for 5 minutes using distilled water.
4. Clean in an ultrasonic cleaner for 5 minutes using alcohol p/a or
isopropanol.
Caution! 
Do not place parts together in the beakers. Wash separately as damage
can occur to the metal surfaces.
5. Rinse in alcohol p/a.
6. First blow dry with a compressed air canister, then dry thoroughly
under an infra-red lamp (15 min to 1 hr) at a temperature of between
80 °C and 100 °C. Do not bake in an oven!

6-4 FEI Limited Rights Data CONFIDENTIAL

 Maintenance: Scroll Pump

Scroll Pump

The pre-vacuum pump is used in the vacuum system which pumps the
microscope, back-ups the TMP and controls the pressure in the
specimen chamber.
It is very important that the pipes to and from the pump are not restricted
in any way. If the pump exhaust pipe is fitted to an internal company
exhaust system it is important that the gas flow is unrestricted by the
system capability, otherwise back pressure can occur which will overheat
the dry pump and deteriorate the pumping speed.

PERIODIC CHECK
Periodic check of scroll pump should be performed every 3 months, or
every month if sample loading is at a high frequency.

CONFIDENTIAL FEI Limited Rights Data 6-5

Maintenance: Compressor and Pneumatics System (option)

Compressor and Pneumatics System (option)

To ensure proper and long-lasting functionality of the Compressor it is

necessary to:
• Check monthly the compressor oil level. During the standstill the
correct level should be between min and max indicators.

FIGURE 6-1 COMPRESSOR OIL LEVEL CHECK

Follow the preventive maintenance schedule (see the separate

compressor manual, page 6).
• Check monthly the condensate amount presence and follow the
Condensate Draining procedure if necessary.

Condensate Draining procedure

1. Vent the the microscope chamber and wait until it is fully vented.
2. Switch off the compressor.
3. Close the compressor Main valve and disconnect the hose from the
compressor outlet.

FIGURE 6-2 COMPRESSOR CONDENSATE DRAINING

4. Fix a piece of a hose no.8 to the small draining valve on the air
receiver.
5. Let the water with oil residue out into the empty bottle.
6. Dispose the oil contaminated material of properly according to the
local regulations.
Note: 
Drain the compressor carefully to prevent spillage.

6-6 FEI Limited Rights Data CONFIDENTIAL

7 SYSTEM OPTIONS

This chapter covers hardware and software that is an option either

integrated in, or accessory to the system.
The items covered here are:
• Optional Detectors
• External Current Measurement (Keithley Picoamper Meter)
• Charge Neutralizer
• Multistub Holder
• Nav-Cam
• Quick Loader
• CryoCleanerEC
Contact your FEI sales representative for more up-to-date information on
system options.

CONFIDENTIAL FEI Limited Rights Data 7-1

System Options: Optional Detectors

Optional Detectors

ANNULAR SCANNING TRANSMISSION

ELECTRONS MICROSCOPY DETECTOR (STEM II)
This is a 8 segments solid-state diode mounted on a retractable arm. It
must be used only with a special sample holder, oriented in an exact
position monitored by a software (see below) or in combination with the
Flipstage. It works best at a slow scan conditions.

FIGURE 7-1 STEM II DETECTOR

Note: 
When the STEM II detector is inserted to the chamber, the stage rotation
and the tilt are locked automatically for the safety.

Holder Arm Installation

Model difference: 
Helios NanoLab 450 S / Helios NanoLab 450 ML uses the Flip stage. 
Helios NanoLab 450 loads the Holder Arm automatically via the LoadLock.
For Helios NanoLab 650 / Helios NanoLab 600i use following procedure:
1. Run the Home Stage (Shift + F3) procedure.
2. Remove all sample holders from the stage plate.
3. Screw the holder arm to the stage plate.

FIGURE 7-2 HOLDER ARM 

Helios NanoLab 450 / Helios NanoLab 600i (650)

7-2 FEI Limited Rights Data CONFIDENTIAL

 System Options: Optional Detectors

Load Sample in Row Holder

1. Place the row holder to the load base (the load base pin is beneath
the position you want to load in / out). Tighten it by the screw knob,
the pin lifts up the spring.
If the pin does not lift up the spring enough to put the sample in,
adjust the lifting height by turning the screw.
2. Insert a sample under the row holder spring.
3. Release the screw knob and the entire row holder from the load base.
4. Repeat steps No. 1 - 4 to load in / out another samples.
5. Put the row holder to the arm.

FIGURE 7-3 ROW HOLDER ON LOAD BASE / 

ROW HOLDER ATTACHMENT INTO ARM (4XX / 6XX)

Inserting and Retracting STEM II Detector

Caution! 
Always take care of any stage movement which could cause a collision
with the STEM II detector. Any collision can cause damage of STEM II.
Before insertion the retractable STEM II detector, the chamber must be
pumped, otherwise the Insert button is not active (a tooltip occurs under
mouse cursor).
When clicking the Insert button the dialogue requires confirmation of the
correct sample holder installation to enable detector insertion. When the
stage is not in a correct position for insertion, another dialogue appears
requiring a confirmation of moving it to the safe position.

Retracting the STEM II is automaticall with the Stopping / Starting the

server or venting the chamber. Otherwise the user can use the Retract
button. When the detector is retracted, the information text is displayed in
each quad which uses it.

CONFIDENTIAL FEI Limited Rights Data 7-3

System Options: Optional Detectors

Settings for STEM II Detector

1. the desired sample in the field of view using the ETD or ICE. Focus
and link Z coordinate to FWD.
2. Select the Detector Settings module / Detector list box / STEM II
detector.
3. Clicking the Insert button causes a dialogue to appear (see above).
• Clicking the Set Up button sets the Bright Field / Dark Field /
HAADF imaging mode (see below) to the quad 1, quad 2 and quad 3
automatically (see the tooltip).
Bright Field imaging
1. Tick the Bright Field radio button.
2. Adjust the contrast and brightness. An image should be visible at low
magnification.
3. Change the voltage to suit the contrast necessary through the
sample.
For example: light materials (poly-silicon or silicon oxide) may work
better with 5 - 10 kV to create contrast, whereas dense materials
(metals) may require 10 - 20 kV or higher.
4. Set the desired magnification, fine focus and correct the astigmatism.
Dark Field imaging
1. Obtain a Bright Field image first.
2. Tick the Dark Field radio button.
3. Adjust the contrast and brightness.
HAADF (High Angle Annular Dark Field) imaging
This mode may require higher voltage to create a suitable image as the
angle subtended to the detection diode can be wide. Choosing 2× the
value used for Brightfield is a good guide level.
1. Obtain a Bright Field image first.
2. Tick the HAADF radio button.
HADF Partial imaging
1. Tick the HADF-P radio button.
You can select any combination of HAADF segments by clicking it on
detector diagram. Active segments are highlighted in yellow. HAADF
segments cannot be combined with DF or BF.
Area of active segments can be “rotated” using the arrow buttons (on the
left and right side of the detector diagram) to view orientation contrast
changes etc.
HADF Partial Complementary imaging
1. Tick the HADF-PC radio button.
It gives the signal from complementary segments to those selected in
HADF Partial.

7-4 FEI Limited Rights Data CONFIDENTIAL

 System Options: Optional Detectors

DIRECTIONAL BACKSCATTERED DETECTOR –

CONCENTRIC BACKSCATTERED DETECTOR
(CBS)
The CBS uses concentric segmentation of the detector diode to
distinguish between BS electrons scattered close to the beam axis –
inner segment (preferentially compositional contrast) and electrons
scattered far from the beam axis – outer segment (more topography
signal). Z-contrast mode provides signal collection from all detector
segments.
It is mounted on a retractable arm which can be inserted between the
lens and the sample and it is parked to the pole piece to reduce vibration.

FIGURE 7-4 DIRECTIONAL BACKSCATTERED DETECTOR

Detector Settings
Select the CBS from the Detector Settings module / Detector list box.
Choose the required mode (All / A / B / C / D / Custom) by clicking the
radio button.
The Custom mode is used to define the segments to be used for
detecting. Clicking the + / - sign over particular segment activates it to
add (yellow color) / substract (blue color) the segment signal. When the
segment color is grey (clicking any sign twice), it is switched off.
The Contrast button is accessible only when the CBS detector is
selected in several quads. Clicking it sets the brightness & contrast of
each quad with CBS detector to the same level.
Distribution of electrons collected by detector segments changes with
setting of working distance, lens mode and Beam Deceleration mode.
It is also possible to set different azimuthal segments in particular quads
and thereafter to use the Enhanced Image module / Mix 3 or Mix 4 tab
to mix color coded signals to create color images (see Chapter 5).
When the detector is retracted, the information text is displayed in each
quad which uses it.

Inserting and Retracting CBS Detector

Before insertion the retractable detector, the user needs to check the
following conditions:
• Chamber is pumped.
• The stage must be moved to a safe position for inserting the detector.
The Link Z to FWD feature must be done and the WD must be more
than 2.5 mm.

CONFIDENTIAL FEI Limited Rights Data 7-5

System Options: Optional Detectors

• The loadlock cycle must not be in progres (Helios NanoLab 450).

• The GIS’s (if present) must not be inserted.
If the above conditions are not fulfilled, the Insert button is disabled, a
ToolTip occurs when the mouse cursor is over a disabled Insert button.
The detector will be inserted after the insertion is confirmed and the tilt is
locked. The stage X, Y and R movements have no limitations, Z-axis
movement is limited to 2.5 mm.
Retracting the detector is automaticall with the Stopping / Starting the
server, when venting the specimen chambre and when the Loadlock
cycle starts. Otherwise the user can use the Retract button.

OBTAINING AN IMAGE IN BSE MODE

1. Select the corresponding Detector in a live Quad.
The vCD limits the minimum achievable working distance so it is
disadvantageous for a high resolution imaging.
2. Close the chamber door and pump down the chamber.
3. When the Vacuum is ready, switch on HV and slowly increase the
contrast and brightness to obtain an image.
Note: 
Whenever the Quad BSED is selected, the optical quad is paused
(because the CCD camera infra-red LEDs are switched off not to emit
the photons supersaturating the detector diode).

RETRACTABLE DETECTORS CONTROL

When any retractable optional detector is installed on the system, the
Insert / Retract button is added also to the Detector Settings module /
Detector: CCD to enable the equipment control while working in the
optical quad.

7-6 FEI Limited Rights Data CONFIDENTIAL

 System Options: External Current Measurement (Keithley Picoamper Meter)

External Current Measurement (Keithley Picoamper Meter)

When the Stage menu / External Current Measurement is ticked, it is

expected to have Keithley picoamper meter connected to the External
Connectors panel / Specimen Current connector, which is located at
the back side of the microscope console.

FIGURE 7-5 EXTERNAL CONNECTORS PANEL

In this case the Status module / Speciment current value is N/A and
the meter readout shows actual speciment current.
Note: 
When the Stage menu / External Current Measurement is not ticked,
switch the picoamper meter off or disconnect it!

CONFIDENTIAL FEI Limited Rights Data 7-7

System Options: Fast Beam Blanker

Fast Beam Blanker

This equipment is used to protect sensitive samples from electron beam.

During moving of the beam to the starting point of a new line / frame /
pattern, the beam is blanked.
Note: 
When the Fast Beam Blanker is used, electron current measurement
may be lower than actual value. This inaccuracy is higher at fast
scanning times. To obtain an exact electron current value use the Spot
mode at a sample area, which is not sensitive or importatnt. (see
Chapter 3).

Multi Stub Holder

Helios NanoLab 450

The Multi-stub Holder with 7-stub holding disc is provided with the
microscope as an option.

FIGURE 7-6 MULTI-STUB SAMPLE HOLDER

It has a spring clip fitting and the threaded shaft which screws into the
stage rotation head center and can be securely attached to the stage by
means of the conical locking piece.

TORX DRIVERS
Within the kit are two Torx drivers to complete the fitting of the interfacing
parts. All screws for interfacing connections are Torx. All screws for
clamping sample stubs are of the Hex-key type. The appropriate Hex-
key tool is standard with the system and not found in this kit.

7-8 FEI Limited Rights Data CONFIDENTIAL

 System Options: I-Beam Charge Neutralizer

I-Beam Charge Neutralizer

The FEI I-Beam Charge Neutralizer uses a low energy electron beam to
control charging induced by the ion beam. This allows imaging and
patterning of nonconductive materials and reduces electrostatic
discharge-related sample damage (by spreading electrons on the
sample).
All controls are placed within the Detector page / I-Beam Charge
Neutralizer module. Values could be adjusted even while the beam is off
in the ranges:
• Filament current: from 0 to 1.43 [A]
• Grid voltage: from -5 to +5 [V]
• Beam energy: from 28 to 200 [eV]
1. Verify whether the correct detector / detector mode is used to enable
the Charge Neutralizer usage (see Chapters 5 and 7):
• The ETD can be used with negative Grid Voltage values 
(Custom mode),
• The TLD can be used with with negative Suction Tube Voltage values
(Custom mode),
• The ICE can be used with negative Grid Voltage values 
(SI / Custom mode).
2. Click the Beam On button to switch the Filament current on (the
filament starts to generate electrons and is heated).
3. Start the charge neutralizer by clicking the Unblank button. The Grid
voltage (as indicated on the slider) is now applied to the grid and (in
case of a positive voltage), electrons will be spread via the grid on to
the sample.
4. Optimize imaging by adjusting the values.
5. Click the Beam off button to turn the Charge Neutralizer off.
The software waits for the filament to cool before venting the chamber
is possible (the progress bar shows the cooling progress, which takes
about 7 minutes).

Finding the Optimal Operation Range

• Before adjusting the filament current or beam energy settings, adjust
the grid voltage until the sample is no longer charging (no drift or
flash):
Start with the grid voltage at -5 V, then slowly increase the value until
the image stabilizes.
• The Initial value of beam energy should be about -100 eV.
• The Initial value of filament current should be about 1.15 A.
Note: 
Filament adjustment should be kept to a minimum as this will
decrease the lifetime of the electron gun.
If neutralization cannot be reached at these values, first increase the
beam energy, then adjust the filament current if necessary.
It is advisible to adjust settings after changing:
• Samples,
• System magnification,
• Scan conditions,
• Ion beam current.

CONFIDENTIAL FEI Limited Rights Data 7-9

System Options: I-Beam Charge Neutralizer

Otherwise, if conditions and sample types remain constant, you should

only have to fine-tune your initial successful settings.
The last settings are stored and can be recalled when switching the
Charge Neutralization off / on and also after exiting UI software.
Balancing Electron and Ion Beam Currents
If your image is still too white and lacking details after you have started
the charge neutralizer and slightly reduced the contrast, you probably
have too much electron beam current compared to ion beam current.
The electron beam is desorbing ions from the surface, which masks the
gallium ion-induced signal (the electron-stimulated desorption). To rectify
the problem try following suggestions:
• Reduce the grid voltage to reduce the beam current. The details
should become visible as you achieve the balance between ion and
electron currents.
• Fine-tune the grid voltage settings to a level appropriate for your
application; the exact value is sample-dependent.
• If you continue to reduce the grid voltage you will reach a switch point
where there are just not enough electrons to compensate the
charging anymore. If you have gone below this point slightly increase
the grid voltage again until the charging disappears. Now you have
reached the optimum working condition with the best possible
contrast of your charge compensated secondary ion imaging.
If you are still unsatisfied with the image, adjust the beam energy (50 V,
for example) and check the results.
In case the filament does not start slowly increase the filament current.

Remarks
• Checking that the Charge Neutralizer is functioning can be made
using a glass sample (FEI company part nr 22805 Rev A).
• When patterning is paused the ChargeNeutralizer stays on.
• When a snapshot / photo is performed with the ion-beam while
patterning with the ion-beam is active the ChargeNeutralizer should
stay unblanked.
• When a snapshot / photo is performed with the E-beam while the ion-
beam patterning and ChargeNeutralizer are active, the
ChargeNeutralizer is automatically blanked and unblanked.This will
enable the use of E-beam grabframe during patterning.
• When an E-beam grabframe is performed during ion beam imaging,
the ChargeNeutralizer will blank but not automatically unblank when
switching back to ion beam imaging.
• In iSPI mode the ChargeNeutralizer can not be used. When working
in iSPI mode the detector interlock is not OK because the electron
beam is imaging.

7-10 FEI Limited Rights Data CONFIDENTIAL

 System Options: Nav-Cam (chamber door mounted)

Nav-Cam (chamber door mounted)

Helios NanoLab 650 / Helios NanoLab 600i

This functionality represents a possibility to navigate across the range of the
stage movement area. This is convenient when investigating large area
samples or several samples with the use of any multi sample holder.

CAPTURING NAVIGATION IMAGE PROCEDURE

1. Vent the chamber, open the chamber door and insert a sample.
2. Close the chamber door and set the WD to 4 mm (top sample surface)
with the use of the CCD 4 mm Marker. Do not pump the system!
At this position only the Nav-Cam functionality is correct!
3. Open the chamber door and rotate the navigation camera to point to
the stage.
At this moment the beam and the detector changes to Nav-Cam and
a live imaging of navigation camera is obtained in the last time active
quad (with the resolution of 768 × 512 pixels only).
4. Select the Stage menu / Move Stage to Nav-Cam function to move
the stage to Nav-Cam position. Use this function also when one
moves the stage to a different position to return it back under the
camera.
In case the Preferences… / General tab / Automatic move to Nav-
Cam position item is set to Yes, the stage moves to the 
Nav-Cam position automatically.
CAUTION! 
When the stage is moving to the Nav-Cam position, do not rotate the
camera until the stage reaches the final position, the alignment
setting (see below) could be lost! 
When the Stage movement stops wait about 5 seconds to let the
camera to automatically adjust a brightness & contrast.
DANGER! 
Be aware of a stage movement, do not put fingers to the trajectory!
5. Capture a navigation image (with the high resolution of 3072 × 2207
pixels) by pressing the silver camera button on the top of its body or by
Snapshot or Photo function (see Chapter 4). A green rectangle (or just
a cross) represents a place, where electron beam will aim. The image
could be saved or adjusted like any other image acquired from the
microscope (image enhancement, process etc.).
If sharpness of the navigation image is not sufficient, try to find a Z-
coordinate (about ±1 mm from WD 4 mm) at which an image is sharp
enough and repeat steps No. 3 and 4.
6. Rotate the navigation camera back to its home position (the stage
moves to its last position before venting the chamber), close the
chamber door and pump the system.
Besides a navigation image one can use also the Digital Zoom module
to navigate the stage (see Chapter 3).
When the Preferences… / General tab / Display Stage Map in
Navigation quads item is set to Yes, stage saved positions are
displayed in the Nav-Cam photo (see Chapter 3).
For a dark or shiny specimens a Nav-Cam image quality could be bad. In
this case run the 401 - Nav-Cam AutoBrightness alignment 
(see Chapter 4).

CONFIDENTIAL FEI Limited Rights Data 7-11

System Options: Quick Loader

Quick Loader

Helios NanoLab 650 / Helios NanoLab 600i

The Quick Loader comprises of the following components:
• Gate valve unit with system safety interlocking
• Lead glass door and loading chamber
• Sample sledges and Stage Adapter
• sample stubs of diameters 12.5 mm, 25 mm and 32 mm
• A guided transfer rod with spring mounted bayonet fitting
• Integrated vacuum control (simple pump and vent control)
The Quick Loader was designed for:
• Easy Sample transfer
• Faster sample through-put
• Contamination free chamber environment
• Materials applications

GENERAL DESCRIPTION
The loader can manually load and unload small samples into the SDB /
SEM. The loader is connected to the specimen chamber of the SDB /
SEM and also integrated into the main vacuum system hardware and
software.

The loader consists of a loading rod with set slide and parking position, a
vacuum chamber for loading and unloading the sample carrier (with
sample) onto a bayonet fitting located at the end of the rod. A gate valve
seals the vacuum of the SDB / SEM specimen chamber and can only be
opened when the vacuum of the loader chamber is correct, this being
indicated by a 'OK' labeled LED prompted by an electrical and
mechanical interlock.
The sample carrier can be entered into the main SDB / SEM specimen
chamber by way of the rod and released by the rotating motion of the rod
at a predetermined position on the stage adapter.

7-12 FEI Limited Rights Data CONFIDENTIAL

 System Options: Quick Loader

Loading rod
The loading rod has a pre-machined slot to move in to load or unload a
sample. At each end there is a side slot. There are 2 side slots at the
further end from the vacuum chamber. One is for loading and unloading
the sample carrier in the loader chamber and the other is a parking
position (prevents the rod to be sucked in by the vacuum).
CAUTION! 
Do not unload the sample carrier with gate valve opened! The sample
carrier could drop down from the rod.
At the end of the rod closest to the loader chamber is a large slot for
coupling and de-coupling the bayonet into or out of the sample carrier
when positioned on the carrier adapter.
The bayonet is designed to make a positive and secure connection to the
sample carrier so that it remains horizontal and in a straight line to
connect with the carrier adapter within the specimen chamber.

Gate valve
The Gate Valve has positions that are defined by the following status:
• rotated position of the Gate Valve Lever: LOCK / UNLOCK
The position has to be turned from LOCK to UNLOCK to be able to
move the loading rod IN and OUT
• colored strips on the side of the exposed barrel axis: 
one / two when IN / OUT

• Position 1 - IN and LOCK

• Position 2 - IN and UNLOCK
• Position 3 - OUT
The Gate Valve has a two safety movements.
• it can be placed over the entry hole on the slide
• it can be locked in place by a turn of the connecting knob (securing
the closure of the valve)
A system interlock takes care of correct conditions (system vacuum,
accelerating voltage) for loading and unloading cycles (movement of the
gate valve).

CONFIDENTIAL FEI Limited Rights Data 7-13

System Options: Quick Loader

Controls
There are 2 buttons (the buttons are illuminated while in operation) and 1
indicator lamp:
• The P (pump) labeled button is pressed to pump the loader chamber
to the required vacuum, the stage moves to a loading position at the
same time. If the system reaches appropriate vacuum level, the lever
interlock is released and the gate valve can be opened. The pump
cycle is automatically terminated when the required vacuum is
reached.
• The V (vent) labeled button is pressed once to vent the loader
chamber. The vent cycle continues till the P button is pressed or it is
terminated by time-out. If the microscope chamber as well as loader
is vented then pressing the V button release lever interlock and gate
valve can be opened.
• The indicator lamp labeled OK lights up when vacuum is reached
after pumping. When it goes out this means the wait time has been
exceeded and the appropriate vacuum for a transfer has been lost.
Pressing the P button again will bring the system to vacuum OK
status.
Control buttons are not shining when the system is recovering from
vacuum status transition (e.g. immediately after the load/unload sample,
during venting the system...). After finishing the state transition the
control buttons will be in operation again.

Sample Carrier, Sample Gauge and Stage Adapter

A sample carriers (2 pcs.) are used to hold and transport the sample
from the loader to the specimen stage of the SDB / SEM. The carrier sits
in the stage adapter with a dovetail joint. It is fixed to the loading rod via a
bayonet coupling. The loading rod is decoupled at the bayonet coupling
when the sample carrier is located in the adapter and withdrawn leaving
the sample carrier ready for sample observation.

The Stage Adapter is connected to the rotation base of the FEI stage by
3 hexagonal headed screws. The base of the adapter has 3 highpoints
for a firm 3-point contact to the rotation base to prevent vibration
transmission.
The height of the stage adapter is distinct to the SDB /SEM system it is
used with. The top of the adapter has a dovetail slot for the acceptance
of the sample carrier from the rod loading mechanism.

7-14 FEI Limited Rights Data CONFIDENTIAL

 System Options: Quick Loader

Sample Height
Before mounting the Stage Adapter the stage must be homed with the
chamber door opened.
Only samples that fit the Sample Gauge can be loaded. One sample stub
of diameter up to 32 mm (1 1/4 ") can be used, although standard sizes
of 25 mm and 12.5 mm can also be used. Height can be no greater than
9 mm.
The shuttle clamps with a spring in the dovetail shaped slot of the
adapter. It is fixed to the loader arm via a bayonet coupling. The
maximum pin length of the stubs that can be used is 11 mm (most
common commercial FEI type stubs have a pin length no greater than 8
mm).
The sample transfer position Ztr is not 0, but in practice from 0.5 to
1.0 mm. The achievable Working Distance could be calculated:
• WDmax = 11.9 mm - H (sample height) + Ztr
• WDmin = 1.9 mm - H (sample height) + Ztr
Consequently the minimum working distance in case of a sample with
minimum thickness could be as much as WDmin = 2.9mm. This is too
much for proper HiRes imaging. However by simply mounting the stub
into the shuttle in an elevated position, as in the drawing, the sample can
be brought up to a minimum working distance of zero.

CONFIDENTIAL FEI Limited Rights Data 7-15

System Options: Quick Loader

INSTALLATION
The Quick loader is pre-installed in FEI factory. No special adjustment is
needed only the loading rod was uninstalled for transport.
1. Unpack the lead glass lid.
2. Remove four screws holding the cover of the loading rod feedthrough.
3. Use the same screws to attach the loading rod to the loader chamber.

Loading position
The load / unload position is preset from factory. If a calibration is
needed, run the Quick Loader Alignment at first.

7-16 FEI Limited Rights Data CONFIDENTIAL

 System Options: Quick Loader

OPERATIONS

Loading a sample
1. Mount the sample with fast drying adhesive medium onto the stub.
Allow to dry.
2. Check the sample satisfies the sample limits imposed by placing the
top of the mounting tool over the base mount.
Caution! 
If the sample proves to be too large this has to be addressed before
the sample and carrier should be allowed into the loader chamber.
3. If the sample satisfies the limits, the sample loaded carrier can be
loaded into the loader chamber. The user can either remove from or
place a mounted carrier in the loader chamber by using tweezers for
stubs which will fit around the stub rim.

Rod Loading Sequence

1. While holding the sample carrier on the loading table in the loader
chamber move the rod out of the Parking position to the far left, to the
back of the slot and forward to engage the bayonet into the sample
carrier. Place the rod back into the Parking position after coupling to
prevent the rod slowly creeping forwards.
2. Switch OFF the electron and ion beam accelerating voltage. Retract
the GIS, Omniprobe or STEM modules (if present) to a safe state
(can not be used in combination with loader).
3. Close the loader chamber lid. After the lid is properly closed the P
button starts to shine.
4. Press the P button, the button stops to shine and the pumping cycle
starts, the stage moves to the loading position at the same time.
When the vacuum in the loader chamber is correct the pump light
starts to shine and the OK button lights up indicating operation can
continue. The gate valve lever interlock is released.
5. Turn the Gate Valve knob lever from LOCK to UNLOCK position.
Then carefully pull the knob bar fully out from the first mark on the
knob drum to the second mark. Turn the knob bar to (anticlockwise)
to the LOCK position.
6. Move the loading rod from the Parking position into the chamber
while still holding the rod bar. The Sample Carrier will engage with the
Stage Adapter at the end of the rod travel.
7. Turn the rod bar to the left (anticlockwise) to the base of the slot; pull
back on the rod bar so it travels along the base of the slot, then turn to
the right (clockwise) so that the rod bar is vertical and withdraw it
back to the PARK slot at the far end of the rod guide.
8. Close the Gate Valve by turning the knob bar to the UNLOCK position
and press the knob in to engage the valve over the opening, this can
be seen through the lead glass lid, then turn the knob bar to the
LOCK position to secure the valve. Good practice is to leave the
loader chamber under vacuum.

CONFIDENTIAL FEI Limited Rights Data 7-17

System Options: Quick Loader

Unloading a sample
1. If there is a sample carrier in the loader chamber attached to the
bayonet, remove it (the chamber needs to be vented and the carrier
removed).
2. Switch OFF the electron and ion beam accelerating voltage. Retract
the GIS, Omniprobe or STEM modules (if present) to a safe state
(can not be used in combination with loader).
3. Close the loader chamber lid. After the lid is properly closed the P
button starts to shine.
4. Press the P button, the button stop to shine and the pumping cycle
starts, the stage moves to the loading position at the same time.
When the vacuum in the loader chamber is correct the pump light
starts to shine and the OK button lights up indicating operation can
continue. The gate valve lever interlock is released.
5. Turn the Gate Valve knob lever from LOCK to UNLOCK position.
Then carefully pull the knob bar fully out from the first mark on the
knob drum to the second mark. Turn the knob bar to (anticlockwise)
to the LOCK position.
6. Move the unloading rod from the Parking position into the chamber
while still holding the rod bar. When resistance is found turn the rod
bar to the left (anticlockwise) to enter the bayonet. Push forward and
turn the rod to the right (clockwise) and the bayonet will engage with
the Sample Carrier on the Stage Adapter close to the end of the rod
travel.
7. Withdraw the rod back to the far end of the rod guide and place in the
Parking position. The rod, bayonet and sample carrier are now out of
the chamber and sit in the Loader chamber.
8. Close the Gate Valve by turning the knob bar to the UNLOCK position
and press the knob in to engage the valve over the opening. This can
be seen through the lead glass lid, then turn the knob bar to the
LOCK position to secure the valve.
9. Press V button once. The chamber will be vented and the lid can be
opened. The sample carrier can be released by turning the rod bar to
the far left and pulled back then returned to the parking position.
Remove the sample carrier.
10.Close the loader chamber lid.
11.Press P button to evacuate the loader chamber.
Note: 
In case the sample carrier falls from the loading rod, vent the chamber
with gate valve opened, put the carrier back to a correct position and
close the gate valve. Proceed from the step No. 1.

Loading/Unloading - vented microscope chamber

If the microscope chamber is vented and Loader chamber is evacuated,
press V to vent the loader chamber. After the chamber is vented, you
can:
• press P button to pump the chamber again if needed (store sample
under vacuum condition)
• press V button to release the mechanical interlock of the gate valve
lever. Then you can open gate valve.
Close the gate valve before microscope chamber pumping.

7-18 FEI Limited Rights Data CONFIDENTIAL

 System Options: CryoMAT Loader

CryoMAT Loader

The CryoMAT Loader is in fact the Quick Loader (see above) with the
addition of the Cryo option, which technically can be added after Quick
Loader installation. It is therefore important to become familiar with the
Quick Loader operation prior to using the CryoMAT option.
The CryoMAT Loader is designed for dehydrated sample transfer,
cryogenic cooling, and temperature control within a SEM or DualBeam
instrument. It has single stage transfer, a preset sample temperature
control, and is integrated into the existing SEM or DB vacuum system.
The result is a simpler system to use for less experienced and
experienced Cryo users alike. It is also designed to be used for more
demanding delicate IC sample TEM prep where ambient temperature or
beam conditions cause problems.

FIGURE 7-7 CRYOMAT LOADER BLOCK DIAGRAM

• 1. The Gas flow controller (on a trolley mount) controls the N2

pressure and flow through the cryo components.
• 2. The Heat exchanger cools down the flowing N2 to cryogenic
temperatures. A water trap captures water from the N2.
• 3. The Gas and electrical interface flange introduces the gas pipes
and electrical cables through the chamber wall.
• 4. The Cold trap creates the coldest position in the chamber to trap
condensing water vapor molecules.
• 5. The Cryo stage Holds the sample at cryogenic temperature.
• 6. The Cryo heater & sensor controller allows temperature changes
to the sample, gives temperature feedback to a visual display for the
cold trap and cryo stage.

CONFIDENTIAL FEI Limited Rights Data 7-19

System Options: CryoMAT Loader

1. GAS FLOW CONTROLLER

The gas flow console panel is housed on the top part of the heat
exchanger trolley to control the N2 flowing through the LN2 heat
exchanger for cooling the cold trap and the cryo-stage.
Primary function of this unit is to regulate the gas flow independently to
the cryo-stage and cold trap via the heat exchanger. The N2 pressure is
regulated from the original supply to this unit at 1.5 bar (21.75 PSI) and 5
liters / minute flow rate.

FIGURE 7-8 GAS FLOW CONTROL PANEL

Trolley panel components
• 2× pressure valves for regulation of the
incoming gas pressure
• 2× gas flow regulators 10 l/m scale
• 2× back pressure end valves with
nonclosing action
• 7× gas connections with interconnective
piping
• Water trap heater temperature read out
display with preset controls
• Power supply to drive the temperature
control, display and N2 water heater
• Output socket to N2 water heater + cable
• Temperature controller connection + cable
• Power input cable and connection (at rear).

2. HEAT EXCHANGER AND LN2 DEWAR

The Dewar volume is 12 liters and will be filled with LN2. It accommodates a
central pipe core of four pipes (two in and two out). Gas flows from the gas
flow control to the two incoming pipes and further into the heat exchanger.
At the end of the central core the pipes end as two coils which sit at the
base of the Dewar to create cooling transferred by conduction from the LN2
to the N2 gas flowing in the pipes.

FIGURE 7-9 HEAT EXCHANGER AND DEWAR

Heat Exchanger components
• Stainless steel or aluminium vacuum
container (Dewar)
• Water trap with heater and cable
• Central pipe core with heat exchange coils
at base
• Insulated cold N2 pipes out of the central
core
• Non-insulated warm N2 pipes in to the
central core
• Power supply (housed in trolley)

The insulated pipes coming out of the central core then proceed to the
gas flow and electrical interface flange situated on a chamber port.

7-20 FEI Limited Rights Data CONFIDENTIAL

 System Options: CryoMAT Loader

The cooled gas feeds the cold trap and cryo stage independently before
returning to the interface flange. The return pipes with gas flowing back
from the cryo stage and the cold trap also enter the insulation (neoprene)
so that ice does not form at the port. These continue to the trolley
entering gas connections through the two back pressure valves and then
to atmosphere.

Water Trap
To prevent water entering the cooling system via the N2 gas, a water trap
is designed into the top of the central core of the heat exchanger. The
water trap chamber volume is heated to evaporate the unwanted water
condensing into the trap. An independent power supply house in the
trolley panel drives the heater.

WA R N I N G !
Whenever handling LN2 (the 12 liter nitrogen Dewar and the Heat
Exchanger), wear face and hand protection (face visor and a pair of
thermal protective gloves). Do not touch cold surfaces as this could
result in burns!

Lowering the Heat Exchanger into the Dewar

1. Allow the LN2 to stabilize from boiling after filling before transporting
the Dewar and before lowering the heat exchanger into the Dewar.
2. Lower the heat exchanger into the Dewar slowly and with caution as
the LN2 will boil due to the warm heat exchanger components.

Removing the Heat Exchanger from the Dewar

WA R N I N G !
1. Remove the heat exchanger from the Dewar slowly and with caution
as the core components remains at cold LN2 temperature for some
time.
2. Place the cold heat exchanger core at the side of the Dewar to warm
up. Do not touch the heat exchanger until the ice condensation on it
has completely thawed.
3. Close the lid to the 12 liter Dewar.

4. COLD TRAP
The cold trap protects the sample from water vapor condensing on its
surface while at low temperature. It is suspended by a bracket from the
back of the chamber to one side of the lens cone.
The extension plate can be used (in addition) for even more effective
anti-contamination of the sample. This encircles some of the lens
diameter but is above the GIS needle input level.
Cold Trap components
• Cold trap plate
• Mounting rod and insulator
• Sensor element
• Ground connector
• Swivel bracket
• Extension Plate

CONFIDENTIAL FEI Limited Rights Data 7-21

System Options: CryoMAT Loader

FIGURE 7-10 COLD TRAP

5. CRYO STAGE
Caution! 
The cryo stage can be rotated (because of the connections of pipes and
wires) maximum ± 20°! 
With the cryo stage installed do not use the Home Stage procedure!
The cryo stage is a multi construction allowing samples to be cooled
down to cryogenic temperatures. The supporting components are
insulated from the low temperature by a double ceramic minimized
contact method. The cold part of the stage can be heated so temperature
can be regulated with feedback via a thermal sensor. This allows the cold
temperature of the sample to be carefully chosen.
The sample can be tilted with the cryo stage to 52° tilt for milling in a
Small Dual Beam instrument.
The thermal insulation is constructed to prevent temperature exchange
from the FEI main stage to the sample and so that constant temperature
can be maintained.
The base plate is constructed in two parts so that the cryo stage can be
removed quickly and conveniently without having to break connections
or cut pipes.
The base has three point contact onto the FEI stage to eliminate
vibration and a location pin that connects into the stage table. In this way,
the load position alignment remains valid when remounting the cryo
stage.
The X, Y and Z axes movements are not limited. Tilt is able to go to
maximum but will only be restricted by the presence of the cold trap at
approximately 56° tilt.
Note: 
Moving the sample away from the protection of the cold trap (above the
sample) can cause ice to condense on the sample by water molecules
released from warmer surfaces.

7-22 FEI Limited Rights Data CONFIDENTIAL

 System Options: CryoMAT Loader

The cryo stage can be removed easily and quickly.

FIGURE 7-11 CRYO STAGE CONSTRUCTION

Cryo stage components

• Mounting base plate
• Thermally insulated stage mount
• Heater element to 100°C
• Sensor element
• Ground connector

Cryo Sample Carrier and Cryo Stubs

The cryo sample carrier connects to the loading rod bayonet with the
same mechanism as the ambient sample carrier. Release and
reconnection to the rod is also using the same mechanism as the Quick
Loader.
The cryo sample carrier connects onto the cryo stage within the SEM/
SDB with a “dovetail” device that is spring loaded on the cryo stage.
The sample stub hole is further along the carrier to a depth of 5.0 mm
and of a diameter to accept with close fit a 10.0 mm diameter stub. The
stub hole is terminated before penetration to the lower side of the sample
carrier. A further 3.0 mm hole is drilled into the center of the base of the
10.0 mm stub hole for vacuum pumping purposes.
A small hex screw secures the stub through a threaded hole at the far
end of the sample carrier.
Standard Cryo Stubs
A plain stub type (10.0 mm length × 10.0 mm diameter) is supplied with
the cryo option as this can then be simply engineered with holes or slots
when necessary. It is commercially available as a consumable product
from many SEM accessory suppliers.
Samples are secured by conductive paint on/in:
• a plain stub for mounting regular or irregular samples,
• a slot in the stub can facilitate thin samples or sheet material,
• a drilled hole in the stub can accept viscous liquids, pastes or strips of
material.

CONFIDENTIAL FEI Limited Rights Data 7-23

System Options: CryoMAT Loader

FIGURE 7-12 CRYO SAMPLE CARRIER WITH STANDARD STUB

6. CRYO HEATER & SENSOR CONTROLLER

Temperature Controller
The controller displays actual (red numbers) Cold Trap / Cryo Stage
Temperature. Required (green number) Set Temperature of the cryo
stage could be set by buttons under the display.
The 3 way Temperature Switch position determines a function:
• at Up position the high temperature is preset (SET 2 Warm) for
sample exchange or removing (up to +50° C, default +20° C),
• at Down position the low temperature is preset (SET 1 Cold) for
sample cooling,
• at Center position a temperature control is not in operation.
The cold trap temperature relies on the N2 flow and should be adjusted
from the gas flow controller (–150° C to –190° C). It must always be at a
lower temperature to the sample, approximately 10° C to 30° C
difference.

FIGURE 7-13 TEMPERATURE CONTROLLER DISPLAY

Temperature controller
components
• Free standing box.
• Temperature readout from
Cold Trap.
• Temperature controller/readout
from Cryo stage.
• 3 way temperature switch
(High/Neutral/Low) for Cryo
stage.
• Control interface cable
• Power cable

7-24 FEI Limited Rights Data CONFIDENTIAL

 System Options: CryoMAT Loader

OPERATING THE CRYOMAT LOADER

Note: 
Follow the sample loading / unloading instructions for the Quick Loader
(see above) and become familiar with the process before operating the
CryoMAT Loader.

Mounting the Sample

1. Mount a stub into the sample carrier and secure it by tightening the
hex screw.
2. Mount the sample with strong adhesive medium such as Carbon or
Silver paint onto the stub. Do not use carbon adhesive pads (Tabs)
because their adhesive can become ineffective at low temperature
and may cause the sample to fall off the stub.

Cooling Down the Sample 

(First Time Operation in Session)
3. With the Heat exchanger removed from the Dewar, fill the 12 liter
Dewar with LN2.
4. Switch on the water heater at the back of the Gas flow controller
trolley. Open the pressure regulators and flow meters fully. The back
pressure regulators should always be open and are only used to
create temporary extreme low temperatures not normally in use. They
have built-in safe none closing valves to prevent a closed circuit.
5. Turn on the dry N2 gas at its source and regulate the pressure to 1.5
Bar pressure to the Gas flow controller trolley.
6. Allow 10 minutes to flush the system of any condensed water. Adjust
the pressure regulators to show 5 L/M on the flow meters. Make sure
that the heat exchanger rod is completely dry and void of trapped
water. Carefully immerse the heat exchanger rod into the 12 liter
Dewar. Watch the temperature controller read-outs for the lowering of
temperature.

Balancing the Flow Rate Versus Temperature

This is a procedure using the default temperature settings. Other
temperatures can be used but the cold trap should always be at a lower
temperature (at least 20°C but no greater than 40°C).
7. Wait for the boiling effect to subside before adjusting, this will be seen
as bouncing balls in the flow meter tubes.
8. The Cold trap will reach a lower temperature first because it is a
shorter circuit, the cryo stage will follow. Therefore first regulate the
flow meter to slow down and stop the cold trap at approximately -
160°C. This will probably be between 4 and 5L/M.
9. Immediately regulate the cryo stage gas flow so that it just over
shoots -130°C. This will probably be between 3 and 4.5L/M.
10.Switch the 3 Way Temperature switch down to SET 1 Cold preset
temperature and wait for the system to reach the required
temperature (-130° C, usually after 10 minutes). The cold trap flow
rate may need a small final adjustment and can now be set so that it
stabilizes at a temperature of ~-160° C).
11.The read-outs on the controller box will indicate the temperature
stability at the cryo stage and cold trap. Do not switch on the beams
till the sample is at the necessary low temperature. Once this is stable
viewing or milling can begin on the sample.

CONFIDENTIAL FEI Limited Rights Data 7-25

System Options: CryoMAT Loader

Sample Exchange / Removing

12.When the sample needs to be warmed up to ambient temperature
before being exchanged or removed, bring the stage to a non-tilt
condition and switch off the HV.
13.Switch the 3 Way Temperature switch up to SET 2 Warm preset
temperature and wait for the system to reach the require temperature
(usually after 20 minutes).
During sample exchange keep the cryo stage at the SET 2 Warm
temperature.
14.Follow from the step No. 10 on to proceed with observation.

FINISHING CRYOMAT LOADER OPERATION

Daytime Use
This operation should only take approximately 15 minutes.
1. Bring the stage to a nontilt condition and switch off the HV.
2. Switch the 3 Way Temperature switch up to SET 2 Warm preset
temperature and wait for the system to reach the require temperature
(usually after 20 minutes).
3. Switch the 3 Way Temperature switch to center position (Off).
4. Remove the sample carrier from the SEM/SDB, vent the loader
chamber and remove it from the loader with tweezers.
5. Turn off the N2 gas supply to the 12 liter Dewar unit and wait for the
supply pipes to the chamber interface to become flexible
(approximately 15 minutes).
6. Carefully remove the heat exchanger from the 12 liter Dewar and cap
off the 12 liter Dewar to save LN2.
7. Turn on the N2 gas supply to the 12 liter Dewar unit and warm the
coils at the end of the core with a hair dryer of at least 1000 Watt.
8. When the temperatures on the controller box show ambient
temperatures, stop heating the coils and turn off the N2 gas supply.
Switch off the water trap heater on the trolley panel.

Overnight
Follow the procedure for Daytime Use and skip steps No. 7. and 8.
9. Allow the system to warm up over night.

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 System Options: CryoCleanerEC

CryoCleanerEC

These equipments allow to decrease the contamination level in the

system. The CryoCleanerEC can be efficient to approximately 24 hours
(CryoCleaner – older version – has silver plated Dewar vessel and can
be efficient about 10 hours).
The kit consists of:
• Vacuum vessel, including o-rings, screws
• Vacuum vessel lid
• Nitrogen vessel (Dewar) with cap, including proper warning labels
• Nitrogen vessel stand
• Nitrogen vessel safety Pliers
• Manual

WA R N I N G ! 
This option uses liquid Nitrogen (LN2), which may cause serious
cold burns.

PARTS AND ACCESSORIES

The CryoCleanerEC consists of a Nitrogen vessel that is surrounded by
an outer container - the Vacuum vessel, which is connected to one of the
specimen chamber ports by a vacuum seal. The space between is then
pumped by the microscope vacuum system.

FIGURE 7-14 NITROGEN VESSEL 

VACUUM VESSEL WITH ACCESSORIES

When the specimen chamber (together with the CryoCleaner) is

pumped, liquid Nitrogen is introduced to the Nitrogen vessel. Its outside
cold surface absorbs contaminating products from the specimen
chamber. The vacuum in the specimen chamber improves over a short
period and contamination is now reduced.

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System Options: CryoCleanerEC

Flanges
The Vacuum vessel has special flange enabling to mount it to different
chamber ports with the use of interlink with a desired shape (depending
on the port to be used and the vicinity).

FIGURE 7-15 CRYOCLEANER FLANGES

The interlink flanges can be mounted on by means of the 3 screw-hole

fittings on the perimeter of the vacuum flange. Care must be taken that
the 'O' ring held in the end of the flange is secure, free of dirt and is not
crimped when mounting.

CRYOCLEANER OPERATION
Once mounted the Nitrogen vessel can be placed in the Vacuum vessel.
Secure the two components by fixing the clips to the top of the Nitrogen
vessel and locking the clips down. Take care that the 'O' ring seal on the
Vacuum vessel is secure when joining the two components together.

Dewar Vessel Refilling

WAR N I N G ! 
The handling of LN2 should be performed wearing face and hand
protection in the form of a face visior and a pair of thermal
protective gloves. 
Users must not touch the cold surfaces of the Dewar as this could
result in burns. Use the Safety Pliers provided, when handling the
Nitrogen Vessel.
1. Pump the specimen chamber, the Vacuum vessel is pumped along
with it.
2. When the specimen chamber vacuum is ready (Pumped status),
partially fill the Dewar with the use of funnel (the plastic cap upside
down) and wait until boiling stops.
3. Then fill the Dewar and place the plastic cap on top of the
CryoCleaner. The volume of liquid Nitrogen needed is approximately
500 ml.
Note: 
The LN2 stops boiling very quickly so that no vibration is seen from this
device. If the CryoCleaner needs to be used for longer periods it can be
refilled with LN2.
Note: 
Before re-filling it is recommended to perform Baking procedure (see
below).

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 System Options: CryoCleanerEC

FIGURE 7-16 PLASTIC CAP FILLING POSITION 

PLASTIC CAP OPERATION POSITION

Removing Nitrogen Vessel

WA R N I N G ! 
Use the Safety pliers provided when handling the Nitrogen vessel.
Removing the Nitrogen vessel depends on the level of contamination
found in the specimen chamber. If the level is unusually high then the
CryoCleaner could work continuously till improvement is seen, otherwise
normally after approximately 2 to 3 hours the Nitrogen vessel can be
removed.
Note: 
It is not recommended to leave it inside the vacuum vessel after all
nitrogen evaporates, because contamination evaporates back to the
chamber.
1. Vent the specimen chamber (the excess LN2 starts to boil).
2. Unclip the Nitrogen vessel from the Vacuum vessel. Lift the Nitrogen
vessel out of the Vacuum vessel by the Safety pliers placed under the
ring on the neck of the Dewar cylinder.

3. Place the Lid over the Vacuum vessel to seal it from the atmosphere
(fix the clips). Pump the specimen chamber again, however the
microscope vacuum remains cleaner than before and sample
contamination is still reduced.
4. Remove the cap from the Nitrogen vessel and pour out the excess
LN2 into a suitable container.

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System Options: CryoCleanerEC

WAR N I N G ! 
When the LN2 is removed from the nitrogen vessel, the bottle still
remains at a very low temperature.
5. Place the Nitrogen vessel onto the Stand ready for baking.

Baking Nitrogen Vessel

1. Place the Nitrogen vessel Stand on a suitable heat resistant surface.
2. Place the Nitrogen vessel onto it and use an Infra-red lamp to bake
the base of the bottle. Baking should take place for approximately 2
hours.
Alternatively the Nitrogen vessel can be baked in an oven at 90 °C for
2 hours.
Regenerating the Dewar by heat allows removal of condensed
contamination and subsequent reuse of the vessel.
Note: 
The oven that is used must have a venting system to extract any harmfull
fumes. Alternatively it should be baked in a fume cupboard using an
infra-red lamp.

Replacing Nitrogen Vessel

1. Vent the specimen chamber. Allow the Nitrogen vessel to cool down
before handling.
2. Unlock two clips holding the Vacuum vessel Lid. Remove the Lid from
the Vacuum vessel.
3. The Nitrogen vessel can be placed in the Vacuum vessel, taking care
that the 'O' ring seal on the Vacuum vessel is secure when joining the
two components together. Secure the two components by fixing the
clips to the top of the Nitrogen vessel and locking the clips down.
4. Pump the specimen chamber. The Vacuum vessel is pumped along
with the specimen chamber.

MAINTENANCE
• Keep the 'O' rings clean of dust and fibre particles by inspecting the
Vacuum vessel main 'O' ring on a regular basis. If the Vacuum vessel
is removed frequently from the specimen chamber, inspect the
specimen chamber 'O' ring seal each time.
• Keep the sealing surfaces of the Nitrogen vessel and the Vacuum
vessel Lid clean and free of dust and fibre particles.
• Do not use any kind of vacuum grease on the 'O' rings.
• Wipe outsides of the stainless steel parts to remove finger stains with
a lint free cloth dampened with pH neutral soap solution.

SPARE VESSEL
It is possible to obtain secondary nitrogen vessel kit, which contains:
• Nitrogen Vessel
• Vessel Stand
• Vessel Plug

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