Treatment of fluorinated ethylene propylene (FEP) and polytetrafluoroethylene (PTFE) in ammonia plasmas produced surfaces with very high wettability by water, but on storage in air at ambient temperature, the air/water contact angles increased markedly. The evolution of the surface composition and topography was studied by angle-dependent X-ray photoelectron spectroscopy (XPS), derivatization of amine groups with fluorescein isothiocyanate, scanning tunelling microscopy (STM), and atomic force microscopy (AFM). XPS demonstrated a continuous increase in the oxygen content over periods of weeks; this was assigned to oxidation of trapped radicals and subsequent secondary reactions. In addition, the fluorine content also changed markedly on storage; the XPS fluorine signal suggested that there was a substantial amount of fluoride in the freshly treated surfaces, and this component disappeared rapidly on storage. STM and AFM showed no changes in topography with aging but suggested surface hardening on plasma treatment. The events following treatment of FEP and PTFE in antmonia plasmas are not adequately described by a model involving plasma-induced, instantaneous chemical modification followed by surface restructuring; the surface and sub-surface compositions evolve over a period of several weeks due to the occurrence of oxidative reactions, and these chemical changes interact with the physical process of surface restructuring.