In situ Fourier-transform infrared (FTIR) ellipsometry has been performed on silicon substrates processed in a rf-biased transformer coupled plasma reactor. Plasmas in CHF3, CF4, C2F6, and C4F8 have been used. The reaction layer, which is present on the surface of the silicon wafer during the plasma process, has been analyzed in detail, addressing both chemical composition and thickness. The absolute reliability (expressed in terms of thickness) of the results is of the order of 0.01 nm, which corresponds to 3% of a monolayer. The instabilities of a silicon surface, which have been observed under specific conditions, can be of the order of tens of percents of a monolayer, which clearly illustrates the advantage of using a real in situ technique like FTIR ellipsometry over quasi in situ techniques like x-ray photoemission spectroscopy and Auger electron spectroscopy. For CHF3 plasmas it has been found that, if the bias increases to moderate levels (30-50 V), the fluorocarbon film deposition rate decreases and the silicon etching reaction rate increases. The reaction layer changes from a thick, predominantly CFx polymerlike film to a thin, carbon dominated layer of plasma and etching products showing vibrational absorptions of SIFx, C-C, and CF2. Increasing the bias voltage in a CHF3 plasma has a similar effect as increasing the F/C ratio of the feed gas.