The nanoscale morphology of the active layer in bulk-heterojunction solar cells consisting of regioregular poly(3-hexylthiophene-2, 5-diyl) (P3HT) and methanofullerene([6-6]-phenyl C61 butyric acid methyl ester) (PCBM) was extensively studied using Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), X-Ray Diffraction (XRD) and optical microscopy. Different weight ratios of P3HT:PCBM were investigated as a function of annealing temperature and time revealing the occurrence of crystallization of both components. Firstly, the as-prepared films can be described as a semi-crystalline blend. Secondly, it has been demonstrated that for a short annealing time (5 min) at lower annealing temperatures (75–115 °C) an increased crystallization of P3HT occurs. Thirdly, it has been observed that a prolonged annealing at the given temperature range or a short annealing at higher temperatures (≥ 120 °C) leads to the formation of a new ordered crystalline structure of PCBM. These new ordered structures, a few μm up to 100 μm in length, form a network of needle-like and even fan-shaped crystals. Key-parameters to “tune” this new ordered structure of PCBM are blend ratio and annealing conditions. The growth mechanism of these new PCBM-structures is described by means of diffusion.