Man .. I know what my next hobby project is going to be :)

Dumb question .. I get that the needle scans a surface and you get the quantum tunneling effect between the atom you are "looking at" and the tip of the needle. What I don't get is how one figures out depth. For each X,Y position, do you just keep going down until you touch something, and then move up, and go to the next position? If so, apart from the issue with 1 atom tip, I imagine the next problem would how to increment X and Y by 1 atom.

P.S. I think some of the marketing put out on these things really confuses the issue. Sure .. it gets people excited about science but it gives people the wrong intuition. As a non-physics person, I got a lot out of this article.