In molecular and organic electronic systems, the electrode material has considerable influence on the performance of the resulting device. The advent of scanning tunneling microscopy (STM) and its various spectroscopic extensions has allowed for exploration of the polymer-electrode interface with atomic-scale resolution. Here I present the use of STM to analyze such systems. Specifically, STM and microwave-frequency alternating current STM (ACSTM) of conducting polymers on different substrates can shed new light on how the electrode material electronically affects the adhered polymer structure. The polymers used in this work are polydiacetylene nanowires and poly(3-hexylthiophene) (P3HT) monolayer, bilayer, and thin films. For both polymers, we can use the convolution of electronic and topographic information inherent in STM topography images to extrapolate information about the electronic structure. It is also possible to acquire information about the work function, the density of states (DOS), relative energy level positions, and the differential capacitance via spectroscopic measurements. In particular, capacitance imaging requires a novel technique known as ACSTM that can be used to probe relative carrier concentration. This thesis presents analyses of PDA and P3HT on graphite and molybdenum disulfide. For P3HT thin films, gold and platinum substrates are also studied. The results indicate a strong substrate-dependent charge transfer that is further illuminated through ACSTM and other spectroscopic investigations. In this work, preliminary investigations of photovoltaic P3HT:fullerene films are also discussed.