The surface modification of polyimide (PI) by the irradiation of 3 keV He+, Ne+ and Ar+ ions was studied using XPS and AFM at various ion dose ranging from 1 x 10(14) to 1 x 10(17) ions/cm(2). The change of surface roughness of PI by 3 keV inert ions was closely connected to the change of surface composition. At low doses below 5 x 10(15) ions/cm(2), the surface of polyimide was carbonized by ion irradiations, showing rough surfaces. At higher ion doses, the surface composition was saturated due to the accumulation of damages, and the surface morphology became smoother as compared with the low dose case.