Cobalt silicide films have been prepared by rapid thermal annealing of cobalt layers sputter deposited on silicon substrates. We report on the evolution of silicide phases, surface and interface roughness as a function of the annealing temperature and silicon surface preparation. The characterizations are carried out by atomic force microscopy, X-ray diffraction, X-ray reflectivity, Raman spectroscopy, and transmission electron microscopy. The cleaning procedure of the silicon substrate affects the interface roughness and the silicide thickness, whereas little effects are found on the surface. On the other hand, surface roughness increases with annealing temperature.