We report nanostructure formation by controlling self-organization on Ga-adsorbed and ultra-thin oxide covered Si surfaces. On the Ga-adsorbed surface, we have formed clean Si stripe areas with atomically accurate size by Ga desorption from the step edges. Selective adsorption of Sb on such surfaces makes it possible to form nanoscale lateral p-n junction structures where Ga-adsorbed (p-type) and Sb-adsorbed (n-type) areas exist alternately on the surfaces. On the ultra-thin Si oxide film (<1 nm thickness) surface, we have found the phenomenon that 10 nm-size clean Si areas appear in the focused electron beam (EB)-irradiated areas after heating. After growing and heating Ge film on such surfaces, we have formed 10 nm-size Ge islands at given areas as a result of the selective surface reactions.