Block copolymers are considered to be highly attractive materials with regards to future applications of nanomaterials and nanostructures owing to their self-assembling nature. Block copolymers, when supplied with sufficient energy, phase separate at the nanoscales to form periodically ordered structures in the nanometer-scale range. A diversity of architectures can be accessed via composition control of individual block components. An exciting area of application for block copolymer self assembly is organic photovoltaic devices (OPV‟s) where it is expected that the very high interfacial area of the blocks with ∼10-20 nm domain spacing would be highly advantageous for exciton diffusion and separation. For this purpose BCPs composed of amorphous (non-conjugated) polymers can also serve as a template for directed assembly of nanoparticles. Zone annealing is a well established method predominantly utilized for metallurgical and semi-conductor purification processes, where recrystallization and oriented grain growth occur on the planar front formed by the cooling-edge of the zone. We have previously applied this process to create highly ordered BCP cylinders that are parallel to the substrate with orientational control, long range order and faster ordering kinetics than conventional thermal annealing. In the present paper, we extend this idea to block copolymer - [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) blend system and report how the presence of PCBM nanoparticles influence the micro-phase separation behavior of cylinder forming poly(styrene-b-2-vinyl pyridine) under a dynamic thermal gradient field. A range of scattering techniques have been on the BCP:PCBM blend system, including grazing incidence small angle x-ray scattering (GISAXS) experiments to characterize in-plane and lateral ordering of BCP-PCBM blend system.