The electron microscope works on a fairly simple principle. We know that we can only see objects because of the light that they emit (more specifically, their electrons absorb photons, and then release photons, and we see the released photons). Photons have a "size" that is determined by their wavelength. Electrons also have a wavelength, and that wavelength is smaller than the wavelength of visible light photons. By using the smaller electrons instead of the larger visible light, we are able to see smaller objects in greater detail.
Microfossils are usually fossils of bacterial life, pollen, spores and other things that would normally need a microscope to be seen. However, it's very difficult to get a decent microscopic view of a rock on a typical visible light microscope. By using an electron microscope, we can "paint" a magnified image of the rock's surface on a computer, without worrying about the thickness of the rock or changes in the focal length necessary to view it.