I thought the highest resolution for looking at atoms came from
these microscopes that drag a stylus over the surface (a technology
developed and marketed by a UCSB physicist, thank you).
Plus I have seen pictures (in Sci Am I think) of IBM spelled out
with atoms.
So there seem to be abundant representations of atoms as seen
from the outside, (assuming that seeing by Braille is acceptable).
Of course without seeing the internal structure of that atom, some
might still be skeptical.
The atoms seen are of course of the larger variety. I don't think
anybody has been taking pictures of hydrogen.
--Dave