The self-organized growth of germanium quantum dots on square nanopatterned Si(0 0 1) substrates is investigated by scanning tunnelling microscopy (STM) and grazing incidence X-ray diffraction (GIXRD) techniques. A regular surface patterning in the 10–100 nm period range is obtained by etching an interface dislocation network obtained by the controlled molecular bonding of Si substrates. The depth of the silicon surface profile is increased by a double etching process. Growth experiments are performed by solid source molecular beam epitaxy (MBE), and for deep trenches, germanium growth conditions are optimized to obtain one Ge dot per Si mesa. It is shown that the trench depth and the mesa profile strongly affect the dot size and its coincidence with the initial regular surface network. Anomalous GIXRD measurements are performed to highlight the Ge elastic relaxation and intermixing during heteroepitaxial growth. We report a significant modification in the stress state of Ge dots as a function of thermal annealing after growth.