Molecular systems and devices are an strongly emerging technology. Various devices are already available, while others are still under development. The usage of molecules offers a great advantage to Si-based electronics, the functional groups of the molecules are adoptable allowing to artificially generate a huge variety of different properties and functionalities. However, the fundamental requirements of molecular engineering are not fully developed yet, mainly wellknown molecules with limited functionality are used nowadays. To analyze and create new molecular structures providing, for example, a very high extinction coefficient while maintaining the chemical structure under environmental conditions would allow to create new types of solar cell conversion devices. This chapter introduces and reviews the research activities of the Nanolino-group at the University of Basel in the active field of the usage of scanning probe microscopy techniques to characterize the mechanical and electrical properties of molecular assemblies down to single molecules.