The 3D nanometer scale phase separated morphology of organic solar cells crucially affects performance. We demonstrate that photoconductive atomic force microscopy can provide both surface and subsurface information in operating organic solar cells providing direct correlation between 3D film morphology, local nanoscale optoelectronic properties and device characteristics. P3HT nanowire:PCBM bulk-heterojunction working devices were investigated. The macroscopic solar cell performance improvements upon thermal annealing, such as an increase in the short circuit current, the open circuit voltage and the fill factor, are consistent with observed enrichment of PCBM at the air interface and increased nanowire crystallinity. PC-AFM is able to directly resolve the associated changes in charge transport and collection at the local scale, with an estimated depth resolution of at least 20 nm inside the film.