Hydrogenated microcrystalline silicon (mu c-Si:H) layers about 500 nm thick were deposited in the same run on flat and rough substrates (rms=60 nm) of various chemical nature. This study reveals that the spatial distribution of the microcrystalline/amorphous phases within the layer depends on the substrate's topography. The influence of the chemical nature of the substrate is shown to be preponderant on the layers nucleation. In particular, this study shows that nucleation density is the highest on plasma enhanced chemical vapor deposited silicon dioxide, whereas it is independent of the substrate's surface topography. Finally, the interpretation of Micro-Raman experiments for the evaluation of the respective volume fractions of amorphous/microcrystalline phases in the layers is discussed in relation with their spatial distribution. (c) 2005 Elsevier B.V All rights reserved.