In this study, the three dimensional nanoscale organization in the photoactive layers of poly(3-hexylthiophene) (P3HT) and a methanofullerene derivative (PCBM) is revealed by transmission electron tomography. After annealing treatment, either at elevated temperature or during slow solvent evaporation, nanoscale interpenetrating networks are formed with high crystalline order and favorable concentration gradients of both components through the thickness of the photoactive layer. Such a tailored morphology accounts for the considerable increase of the power conversion efficiency in corresponding solar cell devices