Blends of conjugated polymers with fullerenes, polymers, or nanocrystals make promising materials for low-cost photovoltaic applications. Different processing conditions affect the efficiencies of these solar cells by creating a variety of nanostructured morphologies, however, the relationship between film structure and device efficiency is not fully understood. We introduce time-resolved electrostatic force microscopy (EFM) as a means to measure photoexcited charge in polymer films with a resolution of 100 nm and 100 micros. These EFM measurements correlate well with the external quantum efficiencies measured for a series of polymer photodiodes, providing a direct link between local morphology, local optoelectronic properties and device performance. The data show that the domain centres account for the majority of the photoinduced charge collected in polyfluorene blend devices. These results underscore the importance of controlling not only the length scale of phase separation, but also the composition of the domains when optimizing nanostructured solar cells.