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Recently there has been significant interest in utilizing the self-assembly behavior of block copolymers in conjunction with traditional lithographic processes to develop inexpensive nanoscale patterning in devices such as microchips. However commercial applications require highly ordered arrays with low defect concentrations. Herein we used self-consistent-field theory (SCFT) to develop a theoretical model to investigate defect formation. Three dimensional SCFT based simulation of the equilibration of block copolymer from random initial configuration in a lithographic trench was conducted. The response of defect concentrations to polymer interactions and trench width was investigated. We then investigated free energies associated with defects with the intent of predicting defect prevalence in large scale lithographic applications. Preliminary analysis of defects suggests that they can be characterized as either edge dislocations or disclination pairs. Further work will attempt to ascertain the response of these fundamental defect formations to variations of the system parameters, search for the optimal parameter values which eradicate, or at least minimize to an acceptable level these defective formations and evaluate lower limits for defect concentrations in real world systems.