The application of biologically inspired organization principles to artificial environments opens up intriguing vistas for the design of complex interfaces. Here we focus on well-defined metal surfaces serving as platforms to handle molecular building blocks with specific functionalities. We employ scanning tunneling microscopy for molecular-level imaging of both single molecules and self-assembled systems, whereas scanning tunneling spectroscopy captures the pertaining electronic properties. Distinct nanoarchitectures, such as biomoleular gratings, metal-organic arrays and porous nanomeshes, are realized through molecular recognition and selective hydrogen bonds, zwitterionic or metal-ligand interactions. Complementary insight from space-averaging techniques and computational modeling allows for the comprehensive assessment of structure-functionality correlation, notably including quantum confinement, chemical reactivity and magnetism. It is suggested that this supramolecular engineering strategy provides a versatile rationale to design unique nanosystems. Their tunable structural and functional characteristics bear promise for future technological applications.