> I assume it could only scan the surface It's not just the surface. It depends on the technique and the microscope, but all the atoms between where the beam e

> I assume it could only scan the surface It's not just the surface. It depends on the technique and the microscope, but all the atoms between where the beam enters and leaves the sample will contribute in some way (though you can have a narrower depth of focus that basically images a few layers at a time, and you can image that way). > unless you scrapped the object away layer by layer. So a complete scan would be destructive. There are other techniques that almost do exactly that! e.g. a SEM (not to be confused with a (S)TEM) can be equipped with a focused ion beam to selectively remove material from your sample. Sadly it's not possible inside a (S)TEM though, at least not today. But that doesn't mean your (S)TEM imaging is non-destructive. The electron beam itself can knock-off lighter atoms, and will seriously damage your sample if you leave it there long enough (and not in a controlled way, so you couldn't use this to purposefully remove layers from your sample). This is especially problematic for anything biological.