A computer implemented method includes obtaining at least one current spectrum with an in-situ optical monitoring system, comparing the current spectrum to a plurality of different reference spectra, and determining based on the comparing whether a polishing endpoint has been achieved for the substrate having the outermost layer undergoing polishing. The current spectrum is a spectrum of light reflected from a substrate having an outermost layer undergoing polishing and at least one underlying layer. The plurality of reference spectra represent spectra of light reflected from substrates with outermost layers having the same thickness and underlying layers having different thicknesses.