Atoms look like very very tiny spheres (or more like cones when on a surface), although there is no way to see this with an kind of optical microscope. However, there are imaging techniques, such as something called STM, or scanning tunneling microscopy, that allows you to see the shapes of atoms. The shape of the atom is determined only by the shape of the electron cloud surrounding it. Using STM, you can map out the shape of the electron cloud by using a metallic tip that interacts with the electrons in the atom, allowing you to see where they are. As the tip moves over the sample, a current, called a tunneling current, is passing from the atoms to the metallic tip. The amount of current is extremely sensitive to the distance from the atom to the tip. So, as you move the tip around over the atoms, you can map out the shape and size of atoms.