The directed self-assembly of block copolymers in cylindrical holes is a promising technology for lithographic patterning, particularly in the context of vertical interconnect accesses. While the hole-shrink process for single cylinders has been extensively explored, the proliferation of morphological defects remains a significant technological barrier. We use a coarse grained model to explore morphologies that form within cylindrical confinements for combinations of template surface energies. We identify metastable defect morphologies, in addition to the desired cylindrical morphology, in majority-wetting sidewall templates. We use our coarse-grained model and the string method to identify transition pathways between defective morphologies and the cylindrical morphology to elucidate the mechanism of defect annihilation within the confinements; the transition pathway from a disordered state is also identified. This work demonstrates that the minimum free energy path for the formation of a cylinder goes through defective morphologies and that designing confinements can eliminate these undesirable transition states.