A near contact atomic force microscope operated at low-temperature is used for vertical manipulation of selected single atoms from the Si(111)-(7 x 7) surface. The strong repulsive short-range chemical force interaction between the closest atoms of both tip apex and surface during a soft nanoindentation leads to the removal of a selected silicon atom from its equilibrium position at the surface without additional perturbation of the (7 x 7) unit cell. Deposition of a single atom on a created vacancy at the surface is achieved as well. These manipulation processes are purely mechanical, since neither bias voltage nor voltage pulse is applied between probe and sample. Differences in the mechanical response of the two nonequivalent adatoms of the Si(111)-(7 x 7) with the load applied is also detected.