Molecular engineering of low-dimensional materials exploiting controlled self-assembly and positioning of individual atoms or molecules at surfaces opens up new pathways to control matter at the nanoscale. Our research thus focuses on the study of functional molecules and supramolecular architectures on metal substrates. As principal experimental tools we employ low-temperature scanning tunneling microscopy and spectroscopy. Here we review recent studies in our lab at UBC: Controlled manipulation of single CO molecules, self-assembled biomolecular nanogratings on Ag(111) and their use for electron confinement, as well as the organisation, conformation, metalation and electronic structure of adsorbed porphyrins.