In this work we report a study on the formation on Ge nano-islands deposited by MBE on Si (001). Blank Si wafers were used to deposit different doses of Ge at 500 C or a constant dose at temperatures ranging in between 500 and 650 C. The use of AFM, EF-TEM, RBS and SEM techniques allowed an extensive characterization of our samples, giving evidence of the influence of experimental parameters on the shape, distribution and composition of the islands. In particular we found that the expected Si-Ge interdiffusion with temperature produces a Si-rich layer on top of the nanostructures (Fig. 1). Morever, to study self-organization mechanisms, we used MBE Ge deposition on Ge ion implanted patterned substrates. The substrates were masked by lithography obtaining circular holes in the range 0.5-1 microns. Before removing the oxide from the bottom of the holes, Ge+ at 75 keV with doses of 1e16 and 2e16 cm-2 …