The structural and electronic properties of molecular layers on surfaces are driven by intermolecular and molecule-surface interactions. This thesis contributes to decipher the role they play in the formation of molecular complexes and explores on the electronic and magnetic properties of the resulting nanostructures with sub-molecular resolution. By means of Low Temperature Scanning Tunneling Microscopy and Spectroscopy (LT-STM and STS), we have investigated two examples of bi-molecular

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... ultra-thin films adsorbed on a Au(111) surface: i) C60 and TPC, and ii) TTF and TCNQ. Density Functional Theory (DFT) calculations of the molecular systems have been employed to corroborate some of the experimental findings. The individual growth of TPC molecules is extremely dependent on the surface temperature. At a low threshold temperature of 80 K, TPC self-organizes in stable molecular clusters that assemble in multilayer islands driven by the TPC three dimensional shape, which favors intermolecular pi-interactions. The mixing with C60 results in the formation of heteromolecular phases that exhibit different patterns based on inclusion complexes mediated also by pi- interactions. Local STS measurements reveal a strong dependence of the C60 electronic properties on the molecular neighborhood, detected as a shift of the molecular orbitals. By this shift, we can resolve the polarizability of single molecules and detect a small lifting of molecules from the metallic substrate. The individual growth of TTF and TCNQ leads to two different molecular networks. On the one hand, the adsorption of TTF is mediated by a large charge donation into the surface, resulting in the formation of a lattice of monomers based in long-range repulsive interactions of electrostatic nature. On the other hand, TCNQ interacts weakly with the underlying surface forming highly ordered self-assembled domains. Co- deposition of TTF and TCNQ on Au(111) form highly anisotropic mixed domains where TTF and TCNQ are distributed in a periodic row arrangem [...]