Wafer-scale control of nanofabrication on Si using selforganization processes are described. Unit cells of surface reconstruction, atomic steps, and domain boundaries of the reconstruction can be used as templates to control arrangement of self-organized nanostructures. We demonstrate that atomic-step network can be organized by controlling the step motion during surface atom evaporation, employing etched patterns formed by lithographic technique. Step/domainboundary network can be modified by using step-flow growth. Ge quantum dot network is self-formed on the surface with well organized templates. Strain distribution on the substrate surface is important for the size and shape control of Ge quantum dots. Chemical reaction control plays an important role in fabricating semiconductor-insulator-conductor nanostructures. In Si/Ge nanostructure, reaction selectivities between Si and Ge can be utilized to form oxide and silicide layers at the Si/Ge interfaces.