A near contact atomic force microscope operated at low-temperature is used for vertical and lateral atom manipulations of selected single atoms on semiconductor surface. The precisely controlled short-range chemical force interaction during a soft nanoindentation with the tip apex atom close to the surface leads to the removal and lateral manipulation of a selected surface adatom, and deposition of a single atom on a selected vacancy at the surface. Besides, the precisely controlled short-range chemical force interaction during a near contact raster scan leads to the sequential lateral atom manipulation. These manipulation processes are purely mechanical, since neither bias voltage nor voltage pulse is applied between probe and sample. Using these different two methods, surface atomic structures on the selected regions were successfully modified. [DOI: 10.1380/ejssnt.2006.1]