Synchrotron x-ray scattering and spectroscopy techniques are used to study the self-assembly of molecular structures on functionalized surfaces. The systems include: the adsorption of negatively charged RNA to a negatively charged hydroxyl terminated SiO 2 surface via cation bridging, rod-coil polar nanolayers, orderly-packed micelles and mineralized micelles, metal-phosphonate-based nanoporous molecular films, and SAMs on Si(111) for biosensing applications. We use x-ray reflectivity to measure the electron density profile, x-ray fluorescence to determine the composition, x-ray standing waves to measure the fluorescence-selected atomic density profile, grazing incidence small- and wide-angle x-ray scattering to measure in-plane and out-plane ordering on the angstrom to nanometer length scale. It is the combination of these complimentary in situ x-ray characterization tools combined with scanning probe microscopies that allows for a more complete description of these nanostructured self-assembled systems on various length scales.