An electron microscope is not able to see electrons. It uses an electron beam instead of a light beam to demonstrate objects. By the DeBroglie hypothesis, matter has a wavelength. An electron has a far shorter wavelength than light, so an electron microscope can see things that are far smaller than what a conventional light microscope can see.
Basically, it will image whatever you put in there, but there are a few restrictions. The object to be scanned must be placed in a vacuum, so if it is an object that will be damaged by dramatic changes in pressure it is not a good idea. It also takes a while to scan, so the object must be able to remain perfectly still for up to a few hours. On the smallest scales, people are banned from being in the same room as a microscope, as the vibrations from their voice will ruin the scan. The object you wish to scan must also be small enough to fit in the scanning vault, which is similar to a small safe (at least on the ones I have seen).