Molecular spintronics aims at exploiting and controlling spin-dependent transport processes at the molecular level. Achieving this aim requires not only appropriate molecules, molecular structures and preparation procedures. Equally important is the understanding and engineering of the electronic and spin-dependent interactions between different molecular species, molecule and substrate, as well as molecule and electrodes. These interactions may not only determine the spin-dependent functionality of the molecular structures, but also their integrity on the substrate. Likewise, there may be also a modification of the surface properties below and in the vicinity of a molecule. We have investigated several molecules on different metallic surfaces, among them magnetic Nd doubledecker phthalocyanines, a cubane-type {Ni4} complex with single-molecule magnet properties, and a nonmagnetic triazine-based molecule. For NdPc2 molecules adsorbed on a Cu(100) surface, our scanning tunneling microscopy and spectroscopy studies show specific electronic states of the molecule-substrate complex. We find that the electric field between STM tip and sample must be taken into account to properly describe the electronic states associated with the upper Pc ligand.