That’s covered in the General Questions thread on this. It’s on a copper surface, and the underlying patterns are from the electron clouds surrounding the copper atoms.
It doesn’t see the atoms, it feels their electric charge. It has a very narrow range. It doesn’t show the atoms on the surface because they didn’t move the needle down far enough to see them.
However, you may notice ripples on the surface. These are some of the free electrons in the copper sheet surface. They cluster in these ripple patterns and the needle picks up their shape.
The electrons in a metal are spread out uniformly among the atoms, in a sort of sea. You can’t really say that the electrons belong to any particular nucleus, and so the “surface” is smooth even on scales comparable to the size of individual atoms.