We present a technique to fabricate polymer substrates with locally structured surfaces in the nanometer scale. By ion projection direct cross-linking the surface of a stretched polymer is locally cross-linked and afterwards annealed above the glass transition temperature to induce surface rippling. The rippling periodicity depends on the thickness of the cross-linked surface layer, formed through hydrogen vacancies, which are generated by the ion bombardment. We systematically studied the effect of the projectile mass on the hydrogen vacancy distribution in polystyrene (PS) samples. Simulations revealed a decreasing depth of the maximum hydrogen vacancy numbers by increasing projectile mass. This value can be correlated to the thickness of the cross-linked PS layer, which directly determines the ripple periodicity. An additional Au capping layer was used to further reduce the cross-linked layer thickness to a few nanometers. By this, defined structures with a ripple periodicity of 250 nm were fabricated. In addition, the technique allows inferring the Young’s modulus of thin cross-linked PS layers.