Catalytic hydrogenation of graphite has recently attracted renewed attention as a route for nanopatterning of graphene and to produce graphene nanoribbons. These reports show that metallic nanoparticles etch the surface layers of graphite or graphene anisotropically along the crystallographic zig-zag ‹11-20› or armchair ‹10-10› directions. The etching direction can be influenced by external magnetic fields or the supporting substrate. Here we report the subsurface etching of highly oriented pyrolytic graphite by Ni nanoparticles, to form a network of tunnels, as seen by scanning electron microscopy and scanning tunnelling microscopy. In this new nanoporous form of graphite, the top layers bend inward on top of the tunnels, whereas their local density of states remains fundamentally unchanged. Engineered nanoporous tunnel networks in graphite allow for further chemical modification and may find applications in various fields and in fundamental science research.