Functional nano-templates enable self-assembly of otherwise impossible arrangements of molecules. A particular class of such templates is that of sp² hybridized single layers of hexagonal boron nitride or carbon (graphene) on metal supports. If the substrate and the single layer have a lattice mismatch, superstructures are formed. On substrates like rhodium or ruthenium these superstructures have unit cells with ~3-nm lattice constant. They are corrugated and contain sub-units, which behave like traps for molecules or quantum dots, which are small enough to become operational at room temperature. For graphene on Rh(111) we emphasize a new structural element of small extra hills within the corrugation landscape. For the case of molecules like water it is shown that new phases assemble on such templates, and that they can be used as “nano-laboratories” where many individual processes are studied in parallel. Furthermore, it is shown that the h-BN/Rh(111) nanomesh displays a strong scanning tunneling microscopy-induced luminescence contrast within the 3 nm unit cell which is a way to address trapped molecules and/or quantum dots.