By using reflection high energy electron diffraction (RHEED), atomic force microscopy (AFM), high-resolution transmission electron microscopy (HRTEM) analyses, we show that the well-known Stranski-Krastanov growth mode of Ge/Si(0 0 1) can be modified in a Volmer-Weber one by C pre-deposition on the Si(0 0 1) surface or in a Frank-Van der Merve one by supplying atomic hydrogen during the Ge growth. By tuning the growth conditions and acting on the interplay of surface diffusion, strain and surface energy, morphology manipulations by the growth process control are therefore possible. The Si capping of these Ge self-assembled nanostructures also allows us to point out a correlation between the nucleation mechanism of the Ge or SiGe islands and their associated embedding process. On bare Si surfaces, the final morphology of the embedded Ge film is strongly dependent on the kinetic parameters of the capping layer. Indeed oriented migrations of both Si and Ge atoms are able to smooth or to maintain the islands on the surface. Si diffusions also contribute in a rapid restoration of a planar morphology. On Si(0 0 1)-c(4 x 4) the adatom migrations and consequently the covering mechanism of the Ge islands seems to be governed by the strain mapping related to the C pre-deposited surface. The first stages of the Si capping process have revealed the preservation of the Ge islands associated to an increase of the surface roughness. (C) 2004 Elsevier B.V. All rights reserved.