By combining ion beam experiments and atomistic simulations we study the production of defects in graphene on Ir(111) under grazing incidence of low energy Xe ions. We demonstrate that the ions are channeled in between graphene and the substrate, giving rise to chains of vacancy clusters with their edges bending down toward the substrate. These clusters self-organize to a graphene nanomesh via thermally activated diffusion as their formation energy varies within the graphene moiré supercell.