What part of the atom is actually visible under the microscope?
Basically, you cannot see atoms using optical microscopes. And the reason why can "see" the shapes of atoms under TEM or AFM is that we use a media to interact with atoms and we collect this interaction information and convert it to a image.
Let's take an example. AFM, viz. Atomic Force Microscopy, is used to measure the force between the probe tip and the specimen surface atoms. If you remember, the potential changes when you are separating two atoms. AFM is to measure this force. When the probe tip is scanning across the specimen surface, it interacts with every atom on the surface (need to mention, the tip of the probe actually is one or two atom size, extra extra sharp). So you then will get a collection of atomic forces for every atom. Based on the two atom interaction curve, you can calculate the distances between probe tip and every atom. So you will get a atomic distance profile. And that will be processed and converted into an image that you can see. But you don't see atoms.
As far as I know, make an optical microscope for looking at atoms is now impossible.