Amorphous fluoropolymers (AF) have recently been developed to provide several favorable characteristics not present in the more crystalline materials. However, these polymers have not been fully characterized and reports of surface modification are not extensive. This work presents results of surface analysis and modification with vacuum ultraviolet (VUV) irradiation of Teflon‐AF‐2400 using contact angle measurements, x‐ray photoelectron spectroscopy (XPS), and laser‐assisted Fourier transform mass spectroscopy (FTMS). Results are compared to those for other, more crystalline, fluoropolymers, namely, poly(tetrafluoroethylene) (PTFE) and the copolymer of tetrafluoroethylene and perfluoroalkoxyvinyl ether (PFA). These three fluoropolymers differ in structure and amount of oxygen that they contain. Samples were irradiated for sixty minutes downstream from a helium microwave plasma, in some instances through a LiF crystal filter. In the latter case, modification is due solely to photons with wavelengths greater than 104 nm. For films treated without filters, reduction in the advancing contact angle was greatest for AF‐2400 and least for PTFE. XPS indicated radiation‐induced defluorination for all polymers treated with or without filters. Concurrently, oxygen incorporation occurs upon exposure to air during sample transfer from the plasma reactor to the XPS instrument. Wetting for treated films improved as the ratio of atomic concentrations for oxygen and fluorine, [O]/[F], increased at the surface. As expected, greater modification was achieved with no filter, possibly due to the effect of higher energy photons and/or helium metastable atoms. Small amounts of nitrogen were also incorporated following treatment, upon exposure to nitrogen gas. Laser‐assisted FTMS experiments on VUV‐treated PTFE and PFA samples resulted in a series of high molecular weight fragments (in increments of 50 amu). This was not observed for untreated films analyzed under similar conditions. It is proposed that VUV irradiation tends to crosslink PTFE and PFA films through defluorination of the –CF2– repeating units, while the AF‐2400 is prone to ring cleavage and does not exhibit this tendency toward crosslinking.