Selective epitaxial growth of germanium (Ge) on nano-structured Si(001) wafers is studied to evaluate the applicability of the nano-heteroepitaxy (NHE) approach on Ge-Si system. Based on a gate spacer technology established in advanced silicon microelectronics periodic arrays of nano-scaled Si islands are prepared, where Ge is deposited on top by reduced pressure CVD. The spacing of these structures is 360 nm. The structural perfection of the deposited Ge is investigated by transmission electron microscopy and X-ray diffraction. It is found that SiO2 used as masking material is responsible for the suppression of the desired strain partitioning effect according to NHE. Even for 10 nm oxide thickness, the lattice of Ge layers deposited on Si nano-islands relaxes completely by generation of misfit dislocations at the interface. The occurrence of additional structural defects like stacking faults and micro twins can be controlled by suited growth conditions.