We have investigated the preferential positioning of self-organized Ge quantum dots on Si (001) mesas fabricated in a selective epitaxial growth (SEG) mode of gas-source molecular beam epitaxy. The surface morphology was evaluated by atomic force microscopy, and for the Si SEG structures, showed mass accumulation at the periphery. Using micro-Raman spectroscopic imaging, the strain-field distribution of Si structures was studied before Ge deposition, and the results suggest a tensile strain at/near the periphery of the structure while a compressive strain at the center. These structures were subsequently used as a template for Ge dots, which tended to align along the mesa edge. The strain field distribution on Si mesas is speculated to be the driving force for preferential nucleation of Ge dots.