Among other things, a computer-based method is described. The method comprises receiving, by one or more computers, a plurality of measured spectra reflected from a substrate at a plurality of different positions on the substrate. The substrate comprises at least two regions having different structural features. The method also comprises performing, by the one or more computers, a clustering algorithm on the plurality of measured spectra to separate the plurality of measured spectra into a number of groups based on the spectral characteristics of the plurality of measured spectra; selecting one of the number of groups to provide a selected group having a subset of spectra from the plurality of measured spectra; and determining, in the one or more computers, at least one characterizing value for the substrate based on the subset of spectra of the selected group.