It is difficult to "see" an atom because basically what you can see optically is limited by the wavelength of the light you use to observe it.
Over the years ways to get around this have been developed - most famously the electron microscope that uses beams of electrons.
Now this brings us to the question of what you mean by optically seen.
Now I can look out of the window and see a tree but without a microscope I can't see a bacteria. As we get smaller I need to look with beams of electrons as in the electron microscope or with probes like the scanning tunneling electron microscope.
In the same way Rutherford "saw" the nucleus when some of the radioactive particles he sent into a gold foil bounce right back.
So you have to think somewhat carefully about what you mean by optically seen.
You might also care to look at this
http://www.particlephysics.ac.uk/news/picture- of-the-week/picture-archive/tracks-in-a-hydrog en-bubble-chamber/000329_sm.jpg
These are the tracks made by subatomic particles colliding
Is this seeing?
Just something to think about