Structure and morphology play a critical role in determining the performance of organic photovoltaic devices. In this paper, variation of the postannealing cooling rate is used to create a series of "snapshots" of the vertical and interfacial reorganization processes that occur upon annealing. The data show that slower cooling rates result in significantly enhanced device efficiencies primarily driven by increased short circuit current and fill factor. UV-vis spectroscopy, X-ray diffraction (XRD), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), atomic force microscopy (AFM), and contact angle measurements are used to probe the origin of these improvements. Our results show evidence for a distinct and changing vertical stratification and interfacial structure in the device throughout the annealing process, with both composition and crystallinity varying through the active layer. The implications of these changes are discussed in terms of device properties.