Graphene features a unique combination of exceptional properties and has emerged as one of the most promising nanomaterials for a variety of applications. The ability to structurally modify graphene with nanoscale precision enables the properties to be further extended. By introducing nanopores in the graphene lattice, nanoporous graphene can be used in high-performance electronic devices or as selective membranes for efficient molecular filtering. Although methods for deterministic nanopatterning already exists, key for the implementation of nanoporous graphene is the development of a scalable and customisable method of patterning graphene that does not require any lithographic mask that is introducing defects. In this project, a novel approach using a nanoporous mask and a broad beam of 20 keV Ar ions has been investigated. Masks with 60-600 nm circular pores have been fabricated, and by irradiating suspended graphene membranes grown by chemical vapor deposition (CVD) through the mask, nanoporous graphene has been deterministically generated. The masks are fabricated using electron beam lithography, and the pattern is highly customisable regarding pore size, pore distribution and areal coverage. In addition to perforating the graphene, the ion beam is also observed to significantly reduce the level of contamination on the graphene membrane. The proposed mechanism is the combination of electronic  sputtering of surface contaminants and the random diffusion that follows, with a low nuclear sputtering yield and to-site pinning of contaminants. An extension of this study could include a more comprehensive characterization of the nanoporous graphene obtained as well as further studies on the dependency of beam parameters.