Near-field intensity enhancement enables laser modification of materials with feature sizes below the classical diffraction limit. However, the need to maintain close distances between the objective element and the substrate typically limit demonstrations of this technology to flat surfaces, even though there are many cases where the ability to produce sub-micron features on rough or structured surfaces are needed. Here, we show the use of a new technique, optical trap assisted nanopatterning (OTAN), for the production of nanoscale features on rippled substrates. The ability to position a microbead near-field objective close to the surface without the need for active feedback and control allows one to continuously move the bead across a rough surface without sticking. Sub-micron patterning of polyimide is demonstrated on surfaces with 1.1 μm steps showing good uniformity. Finally, the enabling technology allows for straightforward parallelization where multiple patterns can be created simultaneously over surface.