Regarding collecting all your data into a single file vs a separate file for each scan line: iolite allows you to use both approaches. There are some advantages to each approach. As Rob mentioned, if you are using a mass spectrometer that has timestamp issues, then collecting everything in a single file will reduce the error associated with this. This was a major issue with Agilent files, but if you copy the entire batch folder across (the xxx.b folder), iolite now reads the timestamp from the associated files to get around some of these problems.
However, collecting all your data in a single file does open the possibility that if something happens to that file (e.g. it is somehow corrupted), you lose your entire image. For our setup in our lab, it is simpler to collect everything in one file, and we haven't had any issues with corrupted files (for the last 10 years or so, at least 😀 ).
Regarding setting up scan lines to only cover your sample for CellSpace, how difficult this is will depend on your laser control software. In at least one laser control software, it's as simple as drawing an outline around your sample, and clicking the "Fill with Lines" button. It only takes about a minute or so (depending on how complex your sample shape is). I haven't used the latest version of ActiveView (ESL), and I've never used Chromium (CETAC), so if anyone has had any experience with those, please feel free to share with the rest of us how to set up this sort of experiment.