What do atoms look like?
Yes, we can definitely see atoms in modern microscopes.  I'll try not to get deep into the subject of "seeing", but I will note that most people say they are seeing when they use their eyes to observe objects.  That is, they are using an optical system (eye) consisting of a lens and a detector (retina) and some image processing carried out by a computer (brain).  Thus, any instrument which uses some sort of detector and a computer to turn the signals of that detector into an image we feel comfortable looking at qualifies to me as "seeing in a microscope."  If you're comfortable with that then read on.

My favorite microscope which is capable of seeing atoms is the transmission electron microscope (TEM).  Using a high quality TEM, we can easily resolve objects around an angstrom in size, which is the distance between atoms.  To image a single atom, you also need to have a sample which is only a single atom thick at some point.  This is tough to accomplish but can be done.  Today, images of graphene provide arguably the best "single atom" TEM images.  A seminal paper is here (paywall).  You can also search the internet for graphene images such as this.

In the links above, the images show the shapes of atoms as little blobs, and to a large extent the blobs are more a description of the microscope's ability to focus rather than the shape of the atom itself.  However, the atomic force microscope (AFM) excels at seeing the electrons at the surface of an atom.  With AFM, researchers are even able to image the chemical bonds of molecules sitting on a substrate.  In this case, the image shows the bonds as rods and the atom centers are not really visible.  Chemistry textbooks often show the "shapes" of atoms by drawing the electron orbitals, so in a sense these rods are the shapes of these atoms too.

This just points up that the "shape" of atoms is a non-trivial subject, which is very dependent on how you look at them.