Transparent solar cell systems have garnered a great deal of attention as possible alternatives to silicon-based solar cells. While conventional silicon-based solar cells absorb solar energy in limited frequency ranges, transparent solar cells absorb solar radiation in both the near infrared and ultraviolet regions of the electromagnetic spectrum. The challenge lies in improving the power conversion efficiency from the current 3.5%. It is therefore crucial to have a complete understanding of the electronic and structural properties of the component materials at the nanoscale to considerably improve their performance. For instance, controlling the morphology and electronic properties of the component acceptor and donor materials will have a direct impact on power conversion efficiencies. In this thesis, I present the use of scanning tunneling microscopy (STM) as a primary tool to analyze these materials with atomic scale resolution. The materials used in this work are monolayer graphene grown by chemical vapor deposition (CVD) and poly(3-hexylthiophene) (P3HT) thin films, which have great potential for use in transparent solar cells. This work outlines my findings in understanding and characterizing different substrate effects on graphene film growth, particularly useful for defect analysis and quality control. This thesis also presents analyses of the important role of pre-treatment of the Cu catalyst on the improvement in quality and continuity of graphene films. Further, this thesis also presents the morphological changes occurring in P3HT film crystallinity resulting from solvent mixing and propose an annealing free approach for efficient self-organization of chains via π-π interactions. I propose the use of two methods for quantifying the persistence length of the polymer chains: edge-detection based Hough transform and the worm-like chain model. By optimizing the graphene electrode and the polymer efficiency we hope to move closer to a carbon-based replacement for bulk semiconductor photovoltaics.