We use self-consistent field theory to calculate the energy of defect formation in cylinder-forming diblock copolymers in laterally confining thin channels. We focus on two isolated defects, dislocations and disclinations and explore a wide range of polymer and channel characteristics. Our findings suggest appropriate conditions for the design of optimized graphoepitaxial processes, where defects are limited to very low concentrations. Using the string method, we also investigate the energy barriers and kinetic pathways of the transition from defective to perfect states.