Selective deposition of gold particles on a patterned substrate was studied for fabrication of a single electrons transistor. In the present study, a selective positioning technique was achieved using atomic force microscope (AFM). Various self-assembled monolayers (SAMs) on silicon surface such as hexamethyldisilazane (HMDS) and octadecyl dimethylmethoxy silane (ODMS) SAMs were prepared as a system for AFM lithography. A uniform pattern was engraved on the SAMs. The selective deposition of gold was efficiently accomplished. This gold particle assembly was characterized by AFM.