An electron beam (EB) lithography technique to form patterns directly on a semiconductor crystal surface, without using a resist or an oxide film, combined with molecular beam epitaxy (MBE) growth is described for potential applications to site definition of quantum dots. Periodically arranged submicrometer protrusions on a GaAs wafer surface were observed by EB irradiation from a scanning electron microscope with moderately high vacuum. This protrusion has a caldera shape with a concave on the top. On the other hand, when the GaAs was irradiated with an EB, although not well focused, from reflection high energy electron diffraction gun in an ultrahigh vacuum annealing chamber of MBE, a pit with concave shape was obtained. Clear photoluminescence emission was observed from an InAs ultrathin layer overgrown on the pit area. (C) 2008 American Vacuum Society.