The plasma deposition of hydrogenated and fluorinated amorphous silicon (a-Si:H,F) and silicon-germanium alloys (a-Si,Ge:H,F) from SiF4-H2 and SiF 4-GeH 4-H2 mixtures, respectively, has been studied in continuous (CW) and modulated wave (MW) r.f. discharges. It has been found that the period and duty cycle of the modulated wave strongly affect the plasma composition, the surface homogeneity and the material properties. The plasma-phase characterization, performed by time resolved optical emission spectroscopy (TR-OES), supplies arguments on the origin of emitting species and on their formation kinetics. It has been found that H* and SiFx are formed by a direct electron impact process involving the same species in the ground state. In addition, the surface homogeneity and some material properties are strongly improved by plasma modulation.