Selective growth of Ge on nanostructured Si(001) wafers is studied to evaluate the applicability of nanoheteroepitaxy approaches on the Ge–Si system for photonics applications under particular consideration of possible growth mask materials. A gate spacer technology established in advanced silicon microelectronics is used to generate a periodic array of nanoscaled Si pillars. The spacing of these Si pillars is 360 nm; diameter and height are about 100 nm, which is still above the expected geometrical parameters to obtain a compliant behavior of the Si lattice in the pillars. Ge dots are deposited by reduced pressure chemical-vapor deposition on top of the Si pillars. The characterization is done by different x-ray diffraction methods and transmission electron microscopy. It is found that even 30 nm thick Ge dots are fully relaxed and they exhibit a clear network of misfit dislocations. Significantly thicker Ge dots generate additional structural defects, mainly microtwins. A strain partitioning between Si pillar and Ge dot was not observed. The main reason for this is not the geometry of pillars but the compressive in-plane strain inside the uncovered Si pillar caused by the surrounding SiO2 layer required as masking material to guaranty the selective growth of Ge on top of the pillars only. High temperature diffraction experiments show that a partial annealing of this strain is possible.