In-situ annealing at a high temperature of 640 degrees C was performed for a low temperature grown Si capping layer, which was grown at 300 degrees C on SiGe self-assembled quantum dots with a thickness of 50 nm. Square nanopits, with a depth of about 8 nm and boundaries along < 110 >, are formed in the Si capping layer after annealing. Cross-sectional transmission electron microscopy observation shows that each nanopit is located right over one dot with one to one correspondence. The detailed migration of Si atoms for the nanopit formation is revealed by in-situ annealing at a low temperature of 540 degrees C. The final well-defined profiles of the nanopits indicate that both strain energy and surface energy play roles during the nanopit formation, and the nanopits are stable at 640 degrees C. A subsequent growth of Ge on the nanopit-patterned surface results in the formation of SiGe quantum dot molecules around the nanopits.