In this paper we report a synoptic methodology to evaluate and optimize the long-range order induced by graphoepitaxy of block copolymer (BCP) self-assembly. The authors focus the study on a BCP that produces hexagonally packed arrays of cylinders oriented perpendicular to the substrate with the copolymer film thickness greater than the trench depth. Prepatterned structures used in the graphoepitaxy approach have been generated by e-beam lithography on a commercial hydrogen silesquioxane resist. A suitable surface modification was accomplished by grafting a random polystyrene-r-poly(methyl methacrylate) copolymer on the prepatterned surfaces. The polystyrene-b-poly(methyl methacrylate) was spin-coated and annealed in order to generate the desired self-assembly. Since the self-assembly process is based on a thermodynamic mechanism, the induced defectivity needs to be reassessed with respect to the standard lithographic process. Using the cylinder center coordinates, a Delaunay triangulation is performed to find the nearest neighbors. This triangulation enables us to easily locate the disclinations which are characterized by having a number of nearest neighbors different from six. Thus, the number of defects can be quantified precisely. Additionally, this methodology affords an accurate evaluation of both the optimum mesa and trench critical dimensions yielding defect-free surfaces and may be extended to monitor the robustness of the BCP directed self-assembly process. Such diagnostics are critical in the implementation of large scale industrial processes.