In this thesis, we present Scanning Tunneling Microscopy investigations of two-dimensional supramolecular architectures and metallic nanostructures on pre-structured surfaces. We studied different self-assembled supramolecular architectures formed by linear dicarbonitrile-polyphenyl organic molecules (NC-Phn-CN, n = 3,4,5,6) on the Ag(111) surface. The molecules differ only in their size, which is determined by the number n of phenyl rings incorporated in the polyphenyl chain. The NC-Ph3-CN self-assemble in a chevron pattern; the NC-Ph4-CN form a chiral open network of rhombic cavities; the NC-Ph5-CN self-assemble in a chiral Kagomé lattice; the NC-Ph6-CN self-assembly is characterized by the formation of several different and coexisting architectures, which are chiral open networks of rhombic cavities in addition to a chiral Kagomé lattice. For all NC-Phn-CN molecules, the coordination with cobalt atoms leads to the formation of metal-organic honeycomb nanomeshes. Thus, by changing the length of the linear dicarbonitrile-polyphenyl molecules, we can fabricate metal-organic honeycomb networks with a tunable cavity size. These open networks have been used as templates to host additional molecules. STM was used to study tip-induced motions of these additional molecules in confined environment. The metal-organic networks have been also exploited to steer the formation of cobalt and iron nanostructures. At low temperature (120 K) and low coverage rate, metal nanostructures form preferentially on top of the organic ligands while they decorate the cobalt coordination nodes at 190 K or at higher coverages. Furthermore, the formation of iron nanostructures at the Al2O3/Ni3Al(111) oxide surface is shown. Iron nucleate at specific sites of the Al2O3/Ni3Al(111) network structure and form three-dimensional nanostructures for deposition temperatures of 300 K and two-dimensional for deposition temperatures of 150 K. It is also shown that two-dimensional nanostructures are stable upon annealing up to 350 K, which is of great interest for further studies concerning catalysis. Finally, first attempts for the ordered growth of gold nanostructures on graphene on the Ru(0001) surface are presented. It is shown that the shape of two-dimensional gold nanostructures is influenced by the underlying moiré structure of the graphene/Ru(0001) surface.