fgrieu
Yeah, once you've exposed the silicon chip inside the package, in effect you have what looks like a crater burned through the plastic (epoxy). You can see the entire square silicon chip, with the ends of the lead frame and wires joining to it.
Then once it's all nice and clean, you add a drop of liquid crystal (similar to the stuff inside your laptop screen or LCD watch) into the crater to make a thin coating. Then you shine a focussed scanning beam of polarised laser light over at the right angle and the reflection is either polarised or not- depending in the charge of the bit. In some cases you need to set up a weak electric field across the chip, just like inside a LCD display. You then use a linear CCD pickup with a polarising filter to read the data out. The trickiest bit is aligning everything so you only scan one row at a time. Kinda like an old tv set, line by line. Doesn't take long once it's set up. Used a lot for CPU and ASIC development and fault analysis by big silicon chip companies.
You may have seen video footage of microprocessors with their lids removed ticking away... Also done with a drop of liquid crystal and a ploarising filter.
Here's a pic showing how you disolve away the plastic to expose the chip.
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There are quite a few youtube videos showing the circuits working under the microscope too.