Abstract. Patterning based on directed self-assembly (DSA) of block copolymer (BCP) has been demonstrated to be a cost-effective manufacturing technique for advanced sub-20-nm structures. This paper describes the application of Mueller matrix spectroscopic ellipsometry (MMSE) based scatterometry to optically characterize polystyrene-b-polymethylmethacrylate patterns and Si fins fabricated with DSA. A regression-based (inverseproblem) approach is used to calculate the line-width, line-shape, sidewall-angle, and thickness of the DSA structures. In addition, anisotropy and depolarization calculations are used to determine the sensitivity of MMSE to DSA pattern defectivity. As pattern order decreases, the mean squared error value increases, depolarization value increases, and anisotropy value decreases. These specific trends are used in the current work as a method to judge the degree of alignment of the DSA patterns across the wafer. © The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.