Polymer films with a nanostructured surface have been applied to fabricate anti-reflective polymer films using a soft molding method. Roll-tol-roll linear ion beam processes manufactured nanostructure surfaces on polymer films without a physical mask. When energetic ions collide to the surface of polymer films, a collisional energy transfer resulted in cross-linking, scission, and thermal heating, which induced self-organized nanostructures on polymer surfaces. Inert and reactive gas ions such as argon and oxygen were exposed on PMMA, PET, PEN, PDMS polymer surfaces with an energy range of 100~1000 eV, and a dose of 1015~1018cm-2. The self-organized nanostructures changed shape and amplitude as a function of the ion species, energy and dose. On polymer surfaces, we fabricated nanostructures which has an opposite shape of moth eye. The polymer films were used for a soft mold to squeeze a moth eye structure on UV-curable resins. Anti-reflective structures were transferred successfully to the curable resin. The anti-reflective films showed transmittance values up to 93%. And the soft molding process using the nanostructured films was tested for repeatable production. The repeatable soft molding was possible without the degradation of transmittance property.