Nanoscale heterojunction systems consisting of fullerenes blended with conjugated polymers are promising materials candidates for achieving high performance organic photovoltaic (OPV) devices. In order to understand the phase behaviour in these thin film devices, we have used neutron reflectivity to determine the behavior of model conjugated polymer-fullerene mixtures. Neutron reflectivity is particularly useful for these types of thin film studies since the fullerenes generally have a higher scattering contrast with respect to most polymers. We are studying model bulk heterojunction (BHJ) films based on mixtures of poly(3-hexyl thiophene)s (P3HT), a widely used photoconductive polymer, and different fullerenes (C60, PCBM and bis-PCBM). We have used neutron reflection measurements to determine the film morphology normal to the film surfaces in real device configurations. The novelty of the approach over previous studies is that the BHJ layer is measured with the confining films of PEDOT/PSS and Al in place. Using this model system, we have measured the effect of typical thermal annealing processes on the film development as a function of the polythiophene-fullerene mixtures.