I'm well aware of how scanning tunneling microscopy works.

Here's a quote from the article "Atom Manipulation with the Scanning Tunneling Microscope":

"Manipulation of single atoms with the scanning tunneling microscope is made possible through the controlled and tunable interaction between the atoms at the end of the STM probe tip and the single atom (adatom) on a surface that is being manipulated. In the STM tunneling junction used for atom manipulation, a host of interactions that depend on the electric potentials between the sample and probe tip, the tunneling current, and tip-adatom distance come into play in the atom manipulation process".