In this study, the nanomorphology of fluorenyl hexa-peri-hexabenzocoronene:[6,6]-phenyl C61-butyric acid methyl ester (FHBC:PC61BM) absorber layers of organic solar cells was investigated. Different electron microscopical techniques, atomic force microscopy, and grazing incidence wide-angle X-ray scattering were applied for a comprehensive nanomorphology analysis. The development of the nanomorphology upon sample annealing and the associated change of the device performance were investigated. It was shown that the annealing process enhances the phase separation and therefore the bulk heterojunction structure. Due to π-π stacking, the FHBC molecules assemble into columnar stacks, which are already present before annealing. While the nonannealed sample consists of a mixture of homogeneously distributed PC61BM molecules and FHBC stacks with a preferential in-plane stack orientation, crystalline FHBC precipitates occur in the annealed samples. These crystals, which consist of hexagonal arranged FHBC stacks, grow with increased annealing time. They are distributed homogeneously over the whole volume of the absorber layer as revealed by electron tomography. The FHBC stacks, whether in the two phase mixture or in the pure crystalline precipitates, exhibit an edge-on orientation, according to results from grazing incidence wide-angle X-ray scattering (GIWAXS), dark-field transmission electron microscopy (DF TEM) imaging and selective area electron diffraction (SAED). The best solar cell efficiencies were obtained after 20 or 40 s sample annealing. These annealing times induce an optimized degree of phase separation between donor and acceptor material.