The surface structure and morphology of ion-beam irradiated 6FDA-pMDA films were investigated using atomic force microscopy (AFM). A beam of 140 keV N / ions with a low current density was used in this work. Three irradiation fluences (2 1 10 14 /cm 2 , 1 1 10 15 /cm 2 , and 5 1 10 15 /cm 2 ) were chosen to represent three different regimes of ion-beam influence on material properties based upon previous diffusion and gas permeation results of implanted polyimide films. Detailed roughness and bearing analyses of the AFM images indicate that freestanding polyimide films have deep surface valleys which can extend to a depth of several micrometers. Ion-beam irradiation, even at a small dose, alters the microstructure of the surface layer and forms a modified layer which eliminates the initial deep valleys. The AFM analysis shows that small fluence irradiation induced microvoids in the surface layer of the polymer, and high fluence irradiation resulted in a large number of small-size microvoids in the surface. All of these results agree well with the ion-beam irradiation effects on iodine diffusion and gas permeation properties of the polyimides. A ripple topographical structure with a wavelength of 25 mm and an amplitude of 2 nm was also observed for irradiated samples.