We devised new nanofabrication methods using a manipulation of self-organized Ag clusters on Sb-terminated Si(100) surfaces by a scanning tunneling microscope (STM) tip. Various kinds of nanostructures could be manufactured by dot-by-dot manipulation. We found that two methods could be used for those fabrications; (1) Ag clusters could be detached and redeposited by a field-induced manipulation using an STM tip and (2) Ag clusters could be also detached from the surface via the formation of mechanical point contact between the tip and clusters. These fabrication methods were systematically investigated with variation of manipulation conditions such as a bias voltage and a tip-sample distance.