Hold on, if I had an electron microscope, can I just put in a decapped cheap large format photodiode under it, jack the beam current way up, and start etching trenches on it?

I don't think so: it's a microscope, not a synchrotron. :D

I meant "drawing" on a photoresist layer with a SEM and then wet-etching it. Also all silicon in a photodiode is doped, so the etched parts would be of little use, I believe.