In this manuscript, we investigated the effect of substrate annealing prior to the deposition of the active layer on the morphological, structural and opto-electrical properties of two variations of organic polymer blends of poly (3-hexylthiophene):C-60 fullerene and poly (3-hexylthiophene):[6,6]-phenyl C-61 butyric acid methyl ester films using atomic force microscopy, field emission scanning microscopy, x-ray diffraction and Hall effect measurements. P3HT films deposited on pre-annealed substrates exhibit an enhancement in the crystallization, and an increase in the electrical conductivity and Hall mobility of p-type P3HT. The microscopic morphology reveals self-assembled fibrillar structures due to the suppressed growth of fullerenes clusters induced by the controlled evaporation rate of the solvent. It is proposed that pre-substrate annealing controls the crystallization of P3HT, the phase separation and diffusion of the acceptor material (C-60 or PCBM). (C) 2010 Elsevier B.V. All rights reserved.