In an approach to creating molecular-scale structures on glass surfaces via self assembly, a strongly-dimerizing ureido-[2-(4-pyrimidone)] (UPy) quadruple hydrogen-bonding array was chemically immobilized on silica surfaces by way of a triethoxysilane functionality. The unreacted surface silanols were then thoroughly passivated with a monofunctional organosilane, resulting in isolated UPy binding sites on the glass surface. These binding sites were found to selectively bind the strongly fluorescent perylenediimide (PDI) functionalized UPy molecules from solution, thus non-covalently linking the fluorophore to the surface. The association between the self-complementary molecules was exceptionally strong, both in solution and at the surface, such that effective hydrogen-bonding was retained after most solvent treatments. The binding was also reversible, however, so that washes with polar protic and dipolar aprotic solvents with high hydrogen-bonding capabilities, such as water, alcohols, and DMSO, resulted in the removal of the non-covalently bound fluorophore-tagged UPy. The UPy:UPy dimer system was also investigated in solution, using pyrene intramolecular excimer formation as a monitor of the dissociation of the pyrene heterodimers into homodimers incapable of forming excimers at micromolar concentrations. In addition, the energy transfer process in solution between pyrene and perylenediimide fluorophores linked through UPy dimerization was studied, with the intention using FRET-based measurements on the surface at single-molecule levels in order to determine the distances between UPy binding sites. Energy transfer was found to occur, but the observed photophysical behavior was complicated by possible secondary processes, which steady-state fluorescence measurements were unable to elucidate. The benefit of using this UPy system for attaching molecules to a surface lies in its reversibility of binding and versatility in manner of molecules which van be retained on the modified surface with a strong association. In this way molecular-scale features could conceivably be constructed on a surface by self-assembly, with the option of further chemical reactions to lock them in place, thus creating structures beyond the accessibility range of the conventional lithographic methods.