The achievement of the desirable morphology at the nanometer scale of bulk heterojunctions consisting of a conjugated polymer with fullerene derivatives is a prerequisite in order to optimize the power conversion efficiency of organic solar cells. The various experimental conditions such as the choice of solvent, drying rates and annealing have been found to significantly affect the blend morphology and the final performance of the photovoltaic device. In this work, we focus on the effects of post deposition thermal annealing at 140 degrees C on the blend morphology, the optical and structural properties of bulk heterojunctions that consist of poly(3-hexylthiophene) (P3HT) and a methanofullerene derivative (PCBM). The post thermal annealing modifies the distribution of the P3HT and the PCBM inside the blend films, as it has been found by Spectroscopic Ellipsometry studies in the visible to far-ultraviolet spectral range. Phase separation was identified by AFM and GIXRD as a result of a slow drying process which took place after the spin coating process. The increase of the annealing time resulted to a significant increase of the P3HT crystallinity at the top regions of the blend films. (C) 2011 Elsevier B.V. All rights reserved.