We report on nanometer-scale patterning of single layer graphene on SiO2/Si substrate through femtosecond laser ablation. The pulse fluence is adjusted around the single-pulse ablation threshold of graphene. It is shown that, even though both SiO2 and Si have more absorption in the linear regime compared to graphene, the substrate can be kept intact during the process. This is achieved by scanning the sample under laser illumination at speeds yielding a few numbers of overlapping pulses at a certain point, thereby effectively shielding the substrate. By adjusting laser fluence and translation speed, 400 nm wide ablation channels could be achieved over 100 mu m length. Raster scanning of the sample yields well-ordered periodic structures, provided that sufficient gap is left between channels. Nanoscale patterning of graphene without substrate damage is verified with Scanning Electron Microscope and Raman studies. (C) 2014 AIP Publishing LLC.