The exposure of hexagonal boron nitride single layers to low energy ions leads to the formation of vacancy defects that are mobile at elevated temperatures. For the case of h-BN on rhodium, a superhoneycomb surface with 3 nm lattice constant (nanomesh), a concerted self-assembly of these defects is observed, where the “can-opener” effect leads to the cut-out of 2 nm “lids” and stable voids in the h-BN layer. These clean-cut voids repel each other, which enables the formation of arrays with a nearest neighbor distance down to about 8 nm. The density of voids depends on the Ar ion dose, and can reach 1012 cm–2. If the structures are annealed above 1000 K, the voids disappear and pristine h-BN nanomesh with larger holes is recovered. The results are obtained by scanning tunneling microscopy and density functional theory calculations.