Functional molecules are of great interest for future applications in "molecular nanotechnology". A detailed understanding of the molecular function when being adsorbed on a surface or in contact with other molecules is required. The scanning tunneling microscope (STM) represents a highly suitable instrument for the investigation of such molecules, because it can not only image molecules with submolecular resolution but is also capable to manipulate single molecules by chemical/electrostatic forces or electronic processes. In this talk, various examples of manipulations of single molecules by low temperature STM will be given. The controlled assembly of functional molecules by "on-surface-synthesis" will be presented, whereas the shape of the molecular nanostructures can be precisely tuned by the initial building blocks. By pulling a polymer from a metallic surface, the conductance can be measured for a single molecular wire as a continuous function of the electrode-electrode distance. Finally, the adsorption and growth of such organic nanostructures on inorganic crystallites, thus creating a hybrid system, will be discussed.