The capabilities of charged particle nanopatterning (CHARPAN) for photonic device fabrication are investigated. The CHARPAN tool is a proof-of-concept tool for a multi-ion beam system that the authors used to directly pattern photonic structures into both Si and Ni as well as for maskless exposure of hydrogen silsesquioxane resist. The realized structures have a regular array and show adequate roundness of the holes as well as little sidewall roughness. For the development and a better understanding of the processes they extended and used the IonShaper (R) simulation software. They could achieve excellent agreement between sputtering simulation and experiments. Furthermore, they developed a nonlocal recoil-based algorithm for the simulation of ion beam induced etching and deposition. Simulation results for three dimensional nanopatterning with this algorithm are presented.