We can't "see" individual atoms with light. The wavelength of visible light is too large to resolve individual atoms, but that doesn't mean we can't detect individual atoms using various methods.
X-rays and beams of electrons both have about the right wavelengths to detect atoms and some microscopes based on either can produce images that resolve to show atomic positions. Transmission electron microscopes can "see" individual atoms in some circumstance. More importantly, the structure of crystals can be resolved by interpreting the diffraction of x-rays from the crystal lattice, providing detailed analysis of the 3-dimensional structure of crystals. This is almost a routine way of determining the structures of molecules as complex as proteins. In a sense this is "seeing" atoms (more strictly it is detecting the electron density). But it is a very indirect way of "seeing" and, strictly, you are detecting using a large assemblage of atoms not just one at a time.
There are modern techniques that allow individual atoms to be detected and even manipulated. These are based on the use of very small needles with atom-sized tips. Atomic force microscopy or scanning tunnelling microscopy and other variants can use the controlled movement of these fine needles to measure the force of interaction between the atoms on the tip of the needle and the molecules or atoms on a surface. So what you are "seeing" is the atomic forces generated by the electron clouds in individual atoms the they interact with something else that is also atom-sized.
For example this image shows a sheet of graphene:
And this image shows a single molecule of pentacene (with a model of the structure shown below the actual image):
There is even an amusing animated video by IBM (who invented the atomic force microscopy technique) showing a story told by manipulating the positions of carbon monoxide molecules on a surface.
These techniques have even been used to understand reaction mechanisms by observing what happens to individual molecules.
So we can "see" molecules at atoms by using devices that can measure atomic forces very precisely. In that sense we can see what they "look" like at least from the point of view of other atoms interacting with them.