The work reported here focuses on the role of nanopatterning in strained heteroepitaxy. This study makes use of an atomistic description. The substrates considered here are quite regular arrays of nanornesas that can be got using stress selective etching of the surface of twist bonded samples (Surf. Sci. (2003) 211). How and why strained growth on such substrates significantly differs from growth on flat substrates is demonstrated. The considered systems are Ge/Si 0 0 1, 2 x I reconstructed nanomesa arrays. For a well-defined range of design parameters (mesa width, grooves depth and facets orientations), one gets one single Ge dot per Si plot. The influence of design parameters is emphasized. (c) 2004 Elsevier B.V. All rights reserved.