The change in chemical structure of the top surface layer of thin poly(methylmethacrylate) (PMMA) and polyimide (PI) films (200–1500 Å) during downstream microwave NF3/CF4/O2plasma etching are investigated byinsituFourier transform infrared (FTIR) reflection–absorption spectroscopy. Plasma fluorination of PI by either NF3or CF4leads to significant surface fluorination characterized by the formation of aliphatic fluorine compounds (CFx), acyl fluoride, benzoyl fluoride, acyl hypofluorite, and polyfluorinated benzene. The surface fluorination process is found to be controlled by diffusion in the product layer and the depth of fluorination is estimated from infrared absorbance to be approximately 500 Å. Addition of oxygen leads to a reduction in the fluoride species and the development of broad absorption bands representing oxygenated surface species. The FTIR data are supplemented byexsitux‐ray photoelectron spectroscopy observations and mechanisms for the observed modifications of the polymer surfaces are proposed. The effect of humidity on the plasma‐modified polymers is studied by comparing infrared spectra collectedinsituafter controlled exposure to moisture. PI fluorinated in NF3show no significant changes, whereas a slow but noticeable change in the carbonyl bands is detected for NF3/Ar plasma‐fluorinated PMMA. Addition of oxygen to the microwave plasma increases the sensitivity of the modified polymer to moisture. These observations are interpreted in terms of the wettability of the polymer surface.