When a cylinder forming triblock copolymer thin film is exposed to supercritical carbon dioxide (scCO(2)), the system suffers an order-order phase transition from parallel (C-parallel to) to perpendicularly oriented cylinders (C-perpendicular to). Here, we found that, during the phase transition, defects modify the energetic barriers for nucleation and provide a strong orientational correlation between the configurations of stable and unstable phases. The topological defects in the primitive phase survive the transition, and its population provides a lower bound for the density of defects in the post-transitional phase. Results, based on experiments and mean-field theory, show that control over the orientational order in the primitive phase can be used to manipulate order and defects in the transversely isotropic hexagonal pattern.