CD variations and/or MD variations in scan measurements are determined from spectral components of power spectra of scan measurements taken using two or more scanning speeds. Dominant spectral components having the same spatial frequencies identify CD variations and dominant spectral components having the same temporal frequencies identify MD variations. Dominant spectral components are extracted from a noisy power spectrum (PS) by sorting all spectral components into an ordered PS. A first polynomial representing background noise of the ordered PS is used to set a first threshold. Spectral components of the ordered PS that exceed the first threshold are removed to form a noise PS. A second polynomial representing the noise PS is used to set a second threshold. Spectral components of the PS that exceed the second threshold are identified as dominant spectral components of the PS.