Organic solar cells based on bulk heterojunction architecture have displayed a complex interplay of morphology, interfacial physics and charge transport characterisitics. We are building a multi-layered research program through collaboration and innovation aimed at understanding how these complexities affect organic photovoltaic function. At the core of this research program is the development of novel experimental methodologies that address the fundamental heterogeneity of organic solar cells. Scanning photoionization microscopy (SPIM) is demonstrated as a tool for mapping the local energy structure of the bulk heterojunction with the chemical contrast of resonant multiphoton ionization and the spatial resolution of diffraction-limited excitation. Femtosecond time-resolved SPIM is introduced as a technique for measuring exciton dissociation dynamics in films based on novel directed architectures employing magnetically- directed assembly by functionalized ferromagnetic cobalt nanoparticles. Single molecule microscopy of fluorescent probes deposited on well-defined wide bandgap semiconductors is demonstrated as a tool for investigating the fundamental energy pathways that govern photovoltaic efficiencies. We will present first results obtained from microscopic studies based on these experimental platforms.