Molecules and atoms at material interfaces have properties that are distinct from those found in the bulk. Distinguishing the interfacial species from the bulk species is the inherent difficulty of interfacial analysis. For organic photovoltaic devices, the interface between the donor and acceptor materials is the location for exciton dissociation. Dissociation is thought to occur via a complex route effected by microstructure and the electronic energy levels. The scale of these devices and the soft nature of these materials create an additional level of difficulty for identification and analysis at these interfaces. The transmission electron microscope (TEM) and the spectroscopic techniques it incorporates can allow the properties of the donor-acceptor interfaces to be revealed. Cross-sectional sample preparation, using modern focused ion beam instruments, enables these buried interfaces to be uncovered with minimal damage for high resolution analysis. This powerful instrument combination has the ability to draw conclusions about interface morphology, structure and electronic properties of organic donor-acceptor interfaces at the molecular scale. Recent publications have demonstrated these abilities, and this article aims to summarise some of that work and provide scope for the future.