At the conclusion of flooding into an oil- or gas-bearing reservoir, a significant fraction of the original hydrocarbon in place remains as trapped residual phase. In addition to determining the amount of trapped phase, the microscopic distribution within the pore space of the reservoir rock is important to gain a better understanding of recovery mechanisms, and for the design and implementation of improved or enhanced recovery processes. While the importance of the mineralogy, wettability, pore scale structure and distribution of residual oil is widely acknowledged, little quantitative information on these properties has been directly available. We describe results from an ongoing interdisciplinary study of this problem bridging the molecular-scale, pore-scale and core-scale of rock structure using surface chemical techniques, pore scale x-ray microtomographic imaging, petrographical imaging and experimental analysis on reservoir carbonate material. We first describe the experimental techniques used in this study and review the registration technology which enables one to quantify mineralogy on 3D images through the integration of SEM-EDS with micro-CT methods. We then discuss methods to visualize pore scale oil and brine populations at the pore scale with a particular focus on characterizing native state plugs. In parallel, we characterize the physical and surface chemical characteristics of rock surfaces at the pore-scale and sub-pore scale, and consider the oil-brine-rock interactions giving rise to these states. This interdisciplinary approach provides the foundation for understanding recovery processes and for the development of strategies to alter wettability and improve recovery in reservoirs.