In order to define mechanisms for pulsed-gas plasma enhanced substrate-selective deposition of silicon, the initial stages of microcrystalline silicon (μc-Si) growth by plasma enhanced chemical vapor deposition on both c-Si and glass substrates were investigated by means of atomic force microscopy (AFM) and reflective high energy electron diffraction (RHEED). Differences in initial substrate morphology were reflected in significant differences in film surface morphology in the early stages of growth. AFM images and rms roughness measurements indicated that the initial growth on the c-Si substrate was three dimensional in character. On glass, the initial Si deposits were much more irregular in shape and the tallest features extended over wider areas than the initial deposits on c-Si. The character of the initial growth on glass was partly obscured by the roughness of the substrate, but the appearance of the initial Si deposits suggested a flatter and more two-dimensional character on glass than on c-Si. As the Si deposition progressed, the films on the different substrates developed similar morphology with increasing thickness. On the c-Si substrate, surface coverage was nearly complete at 50 Å. RHEED analysis of the films grown on c-Si revealed the presence of amorphous structure in the early stages of film growth, which began to transition to a randomly oriented μc-Si structure after 40–50 Å of growth. Observed differences in nucleation affirm and clarify proposed mechanisms and limitations for plasma enhanced selective μc-Si deposition. © 1997 American Institute of Physics.