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SE Plus (also available as an upgrade for SE customer) does this, but is limited as shown in the following example (cf. step 6).
Ai (and Ai Studio, both available as upgrade versions, too) do offer the full batch scanning functionality.

How to do batch scanning with a flatbed scanner with SilverFast:

1. Draw a scan frame to match your first slide / image of film strip.
2. Alt+click outside the first frame to generate another of identical size and proportions.
3. Drag it to match your second image.
4. Repeat from (2) for all images that you want to scan.
5. On the general tab of the main control window you switch to batch mode. next step is optional and possible with Ai (Studio) only:
6. Save your frameset for future re-use.
7. Press "Scan" button and tell SilverFast about file naming and image format type to save in.

If you already have an appropriate frameset, you only need to:
5. Switch to batch mode.
6. Select saved frameset.
7. Start Scan.