A method of controlling a polishing operation includes storing an optical model for a layer stack having a plurality of layers. The optical model has a plurality of input parameters, the plurality of input parameters including a first parameter and a second parameter. The second parameter is a polarization angle or a relative contribution between two orthogonal polarizations. A spectrum reflected from the substrate is measured with an in-sequence or in-situ monitoring system to provide a measured spectrum. The optical model is fit to the measured spectrum, or a plurality of reference spectra are calculated using the optical model and a best matching reference spectrum from the plurality of reference spectra is determined.
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