Atomically-flat surfaces are obtained after thin GaAsSb buffer layer growth on GaAs substrates with regular-distributed nano-holes formed after oxide desorption of the local atomic-force-microscopy anode oxidation. Different from the samples with GaAsSb buffer layers, increasing surface root-mean-square roughness is observed for the GaAs-buffered samples with increasing GaAs buffer layer thickness. The phenomenon is attributed to the enhanced adatom migration resulting from the incorporation of Sb atoms. By using the substrates with nano-holes after buffer layer growth, site-controlled self-assembled InAs quantum dots (QDs) are observed with the deposition of a below-critical-thickness InAs coverage of 1.3 monolayer (ML).