The deposition of microcrystalline silicon films has been studied by in situ spectroscopic ellipsometry. We found that both the etching of the amorphous phase at the film growing surface and the rearrangement of the bulk induced by hydrogen diffusion are necessary to explain the long term evolution during deposition and nucleation mechanisms of microcrystalline silicon. The transition from amorphous to microcrystalline silicon deposition occurs through a highly porous phase. The independent control of the deposition and hydrogen plasma treatment times achieved in the layer-by-layer technique is very well adapted to overcome the substrate selectivity. In particular, we show that we can convert an amorphous film into the microcrystalline state.