Because the surfaces of small structures can dominate their properties, implementing functional nanoscale materials depends to a large extent upon understanding and controlling the surface reactivity. This talk will focus on studies of the adsorption of organic molecules at semiconductor surfaces, toward the ultimate goal of controlling the chemical and electrical properties of the substrate. We will describe model studies of molecular functionalization on both flat and nanostructured surfaces. The presentation will begin by examining adsorption on the Ge(100)-2×1 surface. Using a combination of experimental (infrared spectroscopy, X-ray photoelectron spectroscopy) and theoretical (density functional theory calculation, Monte Carlo simulation) methods, we will show how the molecular structure as well as the identity of the reactive moieties of organic molecules can affect the product distribution upon adsorption. We will then present results of a study in which the organic ligands bonded to semiconductor quantum dots (QDs) are used to tune the electronic properties of the QDs. We will describe experimental and theoretical studies of the effects of such interface engineering on the band gap and relative band positions in lead sulfide (PbS) QDs. These ligand-exchanged quantum dots are tested in multilayer colloidal QD solar cells, and the results show that molecular functionalization can be used to achieve enhanced photogenerated carrier collection in the devices.