The present invention includes searching imagery data in order to identify one or more patterned regions on a semiconductor wafer, generating one or more virtual Fourier filter (VFF) working areas, acquiring an initial set of imagery data from the VFF working areas, defining VFF training blocks within the identified patterned regions of the VFF working areas utilizing the initial set of imagery data, wherein each VFF training block is defined to encompass a portion of the identified patterned region displaying a selected repeating pattern, calculating an initial spectrum for each VFF training block utilizing the initial set of imagery data from the VFF training blocks, and generating a VFF for each training block by identifying frequencies of the initial spectrum having maxima in the frequency domain, wherein the VFF is configured to null the magnitude of the initial spectrum at the frequencies identified to display spectral maxima.