Quantum dots (QDs) grown on semiconductors surfaces are actually the main researchers' interest for applications in the forecoming nanotechnology era. New frontiers in nanodevice technology rely on the precise positioning of the nucleation site and on controlling the shape and size of the dots. Novel approaches to form ordered patterns of homogeneous nanostructures are explored: natural patterning induced by surface instabilities (as step bunching of Si(111) or misoriented Si(001) surfaces), standard patterning with high resolution lithographic techniques, implantation of Ga+ ions by Focused Ion Beam (FIB), or in situ substrate patterning by Scanning Tunneling Microscopy (STM). Based on the analysis of STM images we report on growth and arrangement of Ge islands on Si(001) substrates nanopatterned using several different approaches. The first is a natural method based on the regular step bunching that occurs on Si(111) surfaces with different annealing treatments. The second is based on the self organization of a Si(001) misoriented surface covered by a thin layer of a GeSi alloy. The third exploit an array of holes produced by STM lithography. The forth is a tight pattern created by FIB. We analyze the resulting distribution of islands resulting from all these approaches.