One of the major challenges for the reliable use of self-organization phenomena for device applications is to accurately position quantum dots on the surface. A promising way to get ordered dots is to use prepatterned substrates. We show that a combination of focused ion beam (FIB) prepatterned Si(001) substrates and self-assembled Ge quantum dots (QDs) leads to the precise placement of QDs. The technological advantages of this method are to control the Ge dots size and location, and to scale down the interdots distance to ∼20nm. Regarding more fundamental aspects, the accurate control of nanopatterns characteristics allows us to investigate the influence of various experimental parameters on QDs formation. The process proposed consists mainly of three steps: (1) FIB nanopatterning; (2) ex situ cleaning of the FIB-patterned substrate in order to fully remove the Ga contamination before introduction into the molecular beam epitaxy (MBE) chamber; and (3) Ge deposition by solid source MBE. After optimization of the growth parameters, nicely ordered dense arrays of homogeneous QDs are obtained. QDs are organized on the edges of the FIB holes at high temperature or inside the holes at lower temperature. We suggest that two different mechanisms of Ge dots formation are responsible of these results: kinetically limited nucleation at low temperature and stress driven nucleation at higher temperature.