Nanowires comprised of polydiacetylene, a conjugated polymer, have been analyzed at the nanoscale using scanning tunneling microscopy (STM) and spectroscopy. STM analysis shows that these nanowires exhibit unique electronic behavior due to the different substrate electrode materials used, particularly graphite and molybdenum disulfide. The change in charge transfer behavior is evidence of the importance of polymer-electrode interactions. Nanowires are also shown to randomly desorb due to an interaction with the STM tip. A single disruption often results in the entire nanowire desorbing, and the underlying monolayer is reordered within milliseconds. Additionally, spectroscopic data has been acquired using a novel technique called alternating current STM (ACSTM). ACSTM allows for the acquisition of differential capacitance information. Analysis of the nanowires yields a peak in differential capacitance, as is typical of metal/insulator/semiconductor structures. The ACSTM is sensitive to both carrier concentration and dopant type, making it ideal for future metrological applications.