this was a question that friend of mine asked me on one contest I was this weekend. I was sure with the answer but after I said it I was not able to come up with the reason for it, at least I was not sure enough to say something clear.
So what exactly needs to happen for you to see it? There must be a photon which is reflected off the surface. How does this look like anyway on the atomic level? Well the light hits some electron in its way. There is lot of free space so this is why things that are not transparent can be if they are thin enough. The electron absorbs the photon, jumps to higher level (excitation), then it emits photon. Now on what you see depends upon its wavelength. So different materials will like to absorb different wavelengths making the object to have color. You can only change in what orbital you will have the electron so I guess that this is the fundamental difference between various colors of objects (though I did not check it).
So when electron emits the photon you simply do not know what the electron looked like. The only thing that you can get is just photon of some wavelength and there simply is not any way to look on some kind of surface of electron. Another factor is that the light has too big wavelength and you can not observe surface with that because the photon kind of just flows around and when you get to wavelength of the size of atom or smaller, the energy of the photon is so huge that the electron is anyway blown away.
There is nucleus too of course and normally photons do not get there because of this electron cloud around and nucleus is tiny. Otherwise from what I found it seems that again the proton and nucleus as whole is way too small and you can not actually map the surface.
But I was talking only about electrons and nucleus. You can actually see atom as whole. Not by microscope because visible light is way to huge. There is what is called Abbé difraction limit so you have to look for atoms in different way, using for example electrons (electron microscopes) and then recreate the image using some cool physics, this is for example picture of silicon carbide:
And the one below is picture made by IBM of individual atoms that are shaped like the letters of IBM.
So while you can not see the atom, you can observe, not electron though or even the nucleus at least in ordinary way. You can for example measure energy or calculate the shape but you can not see them as physical objects.
Electron microscopes observe how electrons bounce of the surface just like photons.