The authors report on the use of a helium ion microscope as a potential technique for precise nanopatterning. Combined with an automated pattern generation system, they demonstrate controlled etching and patterning of materials, giving precise command over the geometery of the modified nanostructure. After the determination of suitable doses, sharp edge profiles and clean etching of areas in materials were observed. In this article they present examples of patterning on SiO2 and graphene, which is particularly relevant. This technique could be an avenue for precise material modification for future graphene based device fabrication. The technique has the potential to revolutionize the way that very thin, one-atomic layer materials are modified in a controlled and predictable way.