We studied a site-control technique for InAs quantum dots (QDs) on GaAs substrates using a combination of in situ electron-beam (EB) lithography and self-organized molecular-beam epitaxy. On prepatterned square-mesa structures with a dimension of several tens of microns, we were able to control the average density of Stranski-Krastanow QDs. On these mesa structures, submicron holes in an array were formed as preferential growth sites of QDs by EB writing and Cl-2 gas etching. By supplying 1.8 monolayer (ML) of InAs, QDs were formed in the patterned holes without any formation on the Rat region between them. The QD concentration in each hole was dependent on the hole depth, that is, on the density of atomic steps inside holes. In the holes deeper than 50 Angstrom, QDs were so densely formed that carrier tunneling occurred between them. In the shallow holes with 5-6 ML steps, on the other hand, single QDs were formed.