The self-assembly behavior of siloxane based side chain liquid crystalline block copolymer thin films are investigated via grazing incidence small angle X-ray scattering and atomic force microscopy. The as-spun films displayed polystyrene cylinders perpendicular to the substrate and the cylinders reoriented parallel to the surface after thermal annealing. The morphology observed in the as-spun films is resultant from the orientation of the smectic LC mesophase relative to the substrate. Annealing above both the polystyrene glass transition temperature and the smectic to isotropic transition temperature eliminates the influence of the LC phase, leading to a reorientation of the morphology that minimizes the interfacial energy of the system. (c) 2007 Wiley Periodicals, Inc.