We have successfully fabricated nano-structures on passivated Si surfaces and investigated those structures by using scanning tunneling microscope (STM) and atomic force microscope (AFM). Ag nano-dots were formed on Sb-passivated Si(100) surface via self-organization mechanism and the single-electron charging effect was observed by STM at room temperature. Thermal nitridation and subsequent oxygen-induced etching of Si surfaces resulted in the formation of silicon nano-dots using silicon nitride islands as masks. Au/Ti nano-wire was also fabricated via a selective ion etching of Au/Ti thin film using carbon nanotube (CNT) mask. These results suggest new fabrication method of nano-structures using surface chemical reactions without artificial lithography techniques.