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  • 2 booking slots maximum per day and per person (ie. 1h).
  • 6 booking slots maximum per week and per person (ie. 3h).
  • Reservation names must correspond to the operators.

Saved pictures are available on STI network (EPFL local or VPN):

Contents: CMI

  1. System description
  2. Access conditions
  3. Basic operations

I. System description CMI


MERLIN Overview

  1. Electron optical column GEMINI II
  2. Specimen chamber
  3. Semi-automatic loadlock
  4. Control monitors
  5. Dual joystick
  6. Control panel

The CMi SEM MERLIN is composed of a GEMINI II column, a process chamber with a 5-axes motorized stage (X, Y, Z, Tilt and Rotation) and a semi-automatic airlock. The stage is eucentric, which means that all rotation axes intersect the same point. The specimen surface is located at the eucentric point, where the tilt axis meets the beam axis. This guarantees that the focus is maintained when the specimen is tilted at a certain working distance.

Three different holders are available: mono samples, cleaved samples and full 4inch wafer.


The SEM is controlled by the ZeissSmartSEM software operated via a graphical user interface. The system is also fitted with a dual joystick for stage control and specimen navigation and with a main keyboard control panel for direct access to 14 of the most frequently used functions on the SEM.

dual joystick control panel

The GEMINI II column

The GEMINI II column is the area of the Field Emission SEM, where electrons are emitted, accelerated, bundled, focused and deflected. Main characteristics of the GEMINI II optics are the so-called beam booster and an objective lens that consists of a combined electrostatic/electromagnetic lens doublet.


A Schottky field emitter serves as gun (1). Electrons are emitted from the heated filament while an electrical field is excited by applying the extractor (Uext) voltage. To suppress unwanted thermoionic emission from the shank of the Schottky field emitter, a suppressor voltage (Usup) is applied as well. The emitted electrons are accelerated by the acceleration voltage (Ueht).

The beam booster (Ub, booster voltage), which is always at a high potential when the acceleration voltage is at most 20kV, is integrated directly after the anode. This guarantees that the energy of the electrons in the entire beam path is always much higher than the set acceleration voltage. This considerably reduces the sensitivity of the electron beam to magnetic stray fields and minimizes the beam broadening.

Column mode Characteristics Beam path
High resolution

High resolution imaging
The upper condenser (1) has a low excitation which is varied in order to adjust the probe current in a limited range.
  • Electrons interaction effect is minimized
  • High spatial resolution is guaranteed
  • Probe current range is limited
  • crossover free


    Non-conductive materials and polymers imaging
    The upper condenser (1) focuses the beam and creates a crossover above the ebeam-limiting anode aperture (2). The upper condenser is adjusted to modify the probe current.
    The lower condenser (3) is used for aperture matching of the objective lens (4) for optimum spatial resolution.
  • Whole probe current range is accessible
  • crossover

    Depth of Field

    High topography imaging
    The upper condenser (1) focuses the beam and creates a crossover above the ebeam-limiting anode aperture (2). The upper condenser is adjusted to modify the probe current.
    The lower condenser is operated at a higher excitation than in the two modes describes above. This results in a smaller aperture semi-angle. Thus, the depth of field is increased with a slightly reduced spatial resolution.
  • Provide a high depth of field
  • Useful to investigate high aspect ratio samples or to navigate on a tilted specimen
  • depth of field


    Overall view of the sample
    This mode enables you to view the entire 4inch wafer with electrons (EHT on). Useful for finding you sample or test patterns on the wafer

    Available detectors

    The interaction products most frequently used for generation of images in scanning electron microscopy are secondary electrons (SEs) and backscattered electrons (BSEs). For that purpose, three different detectors are fitted to the system.

    Detectors Typical application
    (annular detector)
    Surface structure
    (Everhart-Thornley detector)
    EsB with filtering grid
    (in-column detector)
    Pure material contrast

  • The In-Lens detector is a high efficiency detector for high resolution SE imaging. It is located above the objective lens and detects directly in the beam path.

    The efficiency of the In-Lens detector is mainly determined by the electric field of the electrostatic lens, which is decreasing exponentially with the distance. Thus, the working distance WD is one of the most important factors affecting the signal-to-noise ratio of the In-Lens. As the tilt angle of the specimen surface affects the emission angle of the electrons, you should avoid strong specimen tilting.

  • The HE-SE2 detector is sensitive to SEs as well as BSEs.

    Electrons moving to the detector are attracted by the collector and directed to the scintillator. The collector voltage can be varied in the range between -1000V and +1000V. The collector voltage generates an electrical field in front of the detector thus directing the low energy SEs towards the scintillator. For all standard applications, the collector bias should be set at +300V.

    Selecting a negative collector voltage generates a field deflecting the low energy SEs so that they cannot reach the scintillator and do not contribute to the signal. Only high-energy BSEs contribute to the image generation. This produces a so-called pseudo-backscattered image, which shows pronounced topography, but largely cancels surface properties (edge contrast).

  • The EsB detector is an Energy Selective Backscattered detector suitable for compositional contrast. It is an annular in-column detector that is located above the In-Lens detector. It can detect SEs and BSEs.

    The SEs and BSEs generated at the impact point of the primary electron beam are intercepted by the low electrical field of the column. These electrons are accelerated by the field of the electrostatic lens.

    A small amount of SEs passes through the hole of the In-Lens detector and would be observed by the EsB detector. To prevent detection of the SEs, a filtering grid is installed in front of the EsB detector. By switching on the filtering grid voltage, the SEs will be rejected and only BSEs will be detected. Below a landing energy of 1.5kV, the filtering grid has the additional function of selecting the desired energy of BSEs. The operator can select the threshold energy of inelastically scattered BSEs to enhance contrast and resolution.

    detectors detectors

    II. Access conditions CMI

    • The CMi SEM MERLIN is reserved to the regular CMI users.
    • It is exclusively reserved to the control of processes which have been done with the CMI installation.
    • The maximal booking time per day is 1 hour (so 2 slots).
    • Saved pictures are available on STI network (EPFL local or VPN): "\\sti1files\cmi-transfert\Z15-Zeiss-Merlin".
    • SEM training is focused on safe loading/unloading + main possibilities of the SmartSEM User Interface + basic alignments procedures for quick and easy imaging. Images + detector settings optimizations are not part of the training. Also, EDX analysis is only possible upon additional training and only after SEM imaging is fully confirmed.

    III. Basic operations CMI

    Starting with the ZeissSmartSEM software

    First, the tool needs to be activated by logging onto CMi Zone15 computer with personal access rights.

    On the SEM local computer, the Windows operating system is always open and running through standard CMi session.

    The EM Server, implementing the internal communication between software and hardware, is always running too. It is sometimes minimized to a small element (icon) on the right side of the Windows task bar.

    EM Server window

    Note: If the EM Sever was closed by the last User, Starting the ZeissSmartSEM software will first reload the EM server and recover software/hardware communication.

    Double click on ZeissSmartSEM icon.

    Software Icon

    Alternatively, select Start/Programs/SmartSEM/SmartSEM User Interface. The EM Server Lon On dialogue appears.

    Log On dialogue

    By logging, the SmartSEM user interface opens and is ready to operate the tool. By default, a TV view inside the specimen chamber is shown.

    User interface

    The data zone is a special and useful group of annotation objects which are used to display useful parameters. If it is not open, select View/Data Zone/Show Data Zone from the menu. Alternatively, type Ctrl + d to toggle the data zone.
    All icons from the toolbar run a specific action on the tool:

    Icon Associated function on left click / middle click

    Scanning Icon 1

    Live scanning / Continuous averaging 2

    Scanning Icon 2

    Pixel averaging 3 / Continuous averaging 4

    Scanning Icon 3

    Pixel averaging 6 / Continuous averaging 6

    Scanning Icon 4

    Pixel averaging 9 / Frame integration 5

    Scanning Icon 5

    Frame integration 7 / Frame integration 9
    Icon Associated function on left click

    Specimen change Icon

    Specimen change via the loadlock

    Scanning command Icon

    Faster and slower scanning command

    Freeze/Unfreeze Icon

    Freeze / Unfreeze command

    Normal scanning Icon

    Normal scanning command

    Reduced area Icon

    Reduced area activation

    Screen splitting Icon

    Screen splitting to get two detectors viewing on the same window

    Brightness / Contrast Icon

    Brightness and contrast adjustment (with mouse)

    Chamber scope Icon

    Chamber scope (TV view) activation

    In-Lens / SE2 toggle Icon

    Toggle In-Lens / SE2 detectors

    Magnification / Focus Icon

    Magnification and focus adjustment (with mouse)

    Save image Icon

    Save image to folder


    Press Exchange on the keyboard.


    Follow and perform all instructions of the macro message before clicking OK.
    Clicking OK will start pumping in the airlock and will open the gate.

    The Vent button is used to ventilate the loadlock.

    Be sure the holder is correctly loaded!
    Be sure to screw the rod on the holder!

    Close the door and click OK on the macro message for the pumping to start.
    When correct vacuum is reached, the gate will automatically open.

    Check from the window when the gate is open. The light inside the chamber is automatically switched on.
    Load the sample onto the stage and retract the rod all the way out.
    When loading, visually check from the window what you are doing!
    Be sure the holder is steady on the stage and that it doesn't move when the rod is turned counterclockwise and then retracted.

    Click OK on the previous macro message and click Resume on the keyboard to close the gate.

    Here, there is no need to ventilate the airlock: just click OK on this message.

    Click OK to finish the loading sequence and to proceed with SEM imaging.


    Press Exchange on the keyboard.


    Click OK on the macro message (there is no need to ventilate the airlock now).
    Clicking OK will start pumping in the airlock and will open the gate.

    Check from the window when the gate is open. The light inside the chamber is automatically switched on.
    Unload the sample from the stage and retract the rod all the way out.
    When unloading, visually check from the window what you are doing!
    Be sure the holder is steady in the airlock with the rod fully retracted.

    Click OK on the previous macro message and click Resume on the keyboard to close the gate.
    Follow instructions before clicking OK on the following message.

    The Vent button is used to ventilate the loadlock.

    Unload the sample.

    Close the door and click Store on the airlock for the pumping to start.
    Validate the previous message by clicking OK.

    Click OK to finish the unloading sequence.

    Stage settings and motions

    The Stage Navigation window can be used to initiate XY movement of the stage by double-clicking on the sample holder top view. Be sure to select the correct holder from the list and to adjust the zoom view sliding bar to your needs. All five axes coordinates are reported in this window in order to save specific positioning on the sample if needed.

    The STOP button on the Stage Navigation window or the Break button on the dual joystick can be clicked at any time to quickly stop any engaged motion of the stage.

    stage navigation dual joystick

    Left joystick (Z and T) has to be used with great care: a risk of damaging the tool and/or the specimen is present if hitting the objective lens while driving the stage. Watch the moving stage in TV mode.
    Finding your way on the sample is mainly done by the use of the dual joystick panel, where all five axes can be actuated.

    Sample observation

    The following table may help to find the required settings for your application:
    Detector EHT Typical WD Detector settings Remarks
    3kV- 20kV
    3 - 6mm
    None Avoid strong specimen tilting.

    Surface structure
    100v - 3kV
    2 - 3mm
    100V Max 4mm
    HE-SE2 1kV - 30kV
    Min 4mm
    Collector bias adjustable from -1000V to +1000V.

    Standard applications: +300V

    Pseudo BSE image: -1000V to 0V


    1kV - 5kV
    4 - 6mm
    5kV - 30kV
    Min 6mm
    EsB 1kV - 5kV
    Max 4mm
    EsB grid adjustable from 0V to +1500V.

    Value depends on type of electrons to be detected (approx.):
    <800V : SE +BSE
    >800V: BSE

    Avoid strong specimen tilting.

    Materials contrast

    100V - 1kV 1 - 2mm

    Please, avoid using the arrow keys at the edges of the sliding bar when selecting column current!
    Use either the slide bar, or type the desired valued in directly.

    Useful keyboard shortcuts

    • Ctrl + d : display/hide data zone
    • + (numerical keyboard) : increase the scaning rate
    • - (numerical keyboard) : decrease the scaning rate
    • tab : fine/coarse mode
    • Ctrl + tab : center the sample where click on the picture
    • Ctrl + shift + tab : drag a rectangle on the picture and the system will automatically zoom in and center the sample into it
    • Ctrl + A : annotation tools