The kinetics of surface processes occurring on TiSi2 and CoSi2 thin films in the afterglow of a NF3 plasma are studied. Analysis of the silicide surfaces by x-ray photoelectron spectroscopy and ellipsometry shows that a metal fluoride film forms during NF3 treatment. The thickness of the metal fluoride film on top of CoSi2 at 280-373 K and TiSi2 at T<300 K versus time is described by a parabolic law. The interaction of the silicides with the NF3 plasma in these regions is dominated by the diffusion of fluorine through the metal fluoride film. In the case of TiSi2 at T>300 K, the influence of the TiF4 desorption becomes important. Both Co and Ti fluorides are completely removed in a H2SO4/H2O2 mixture. After this treatment the silicide surface contains only 3-4 nm of silicon dioxide. Based on insight obtained in the fluorination process, the equations describing both the kinetics of CoSi2 and TiSi2 etching and the change of selectivity of SiO2 etching towards the silicides are explained.