A computational procedure is presented to quantify the order achieved in assembled block copolymer films when no disruptive defects are present (i.e., dislocations or disclinations). Both simulated and real systems were used to show that sub-nm variation in the domain position, as well as the corresponding reciprocal lattice vectors, can reduce the accuracy in the quantification of the order of the system. The computational procedure in this work was based on fitting to the measured spatial location of the domain centroids, and incorporated a tolerance factor to account for domain position variation. The procedure was used to analyze the translational and orientational order parameters of block copolymer films assembled on a chemical pattern as well as their corresponding autocorrelation functions. The procedure was applied to a patterned substrate during three stages of a template forming process: an e-beamed patterned photoresist, the domains of a block copolymer directed to assemble on this pattern, and the underlying structure after lift-off. Use of the procedure demonstrated that the order of the block copolymer film could be retained in subsequent processing of the underlying template. (C) 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 2589-2603, 2010