Atoms are really, really small. About a thousand times smaller than the wavelength of light that we see with. The distance between atoms is similarly small as well, and it is impossible to resolve even using optical microscopes.
There are advanced microscopy techniques which allow us to resolve individual atoms in a lattice. Scanning tunnelling microscope is one such instrument. It does not use light to do the imaging and works based on quantum tunnelling. (you can read more about this technique here)
Scientists at the University of California, Los Angeles, have found a way to create stunningly detailed 3D reconstructions of platinum nanoparticles at an atomic scale. They are being used to study tiny structural irregularities called dislocations.
Dislocations and their interaction strongly influence many material properties, ranging from the strength of metals and alloys to the efficiency of light-emitting diodes and laser diodes.