1. In an inspection system for detecting defects in devices of any type having either random, repeating or mixed patterns within the same device, said inspection system includes first and second fields of view each positioned along a different optic axis, the first field of view creates a spatial domain pixel map of a portion of a first substrate pattern; and said second field of view provides a spatial domain pixel map against which said first substrate pattern is to be checked from either a pre-stored pixel map of the desired pattern, a scaled drawing of the desired pattern, a repeating pattern within the same device on said first substrate as in said first field of view, a pattern within a different device on said first substrate as in said first field of view, or a second substrate pattern; a method for detecting defects in said first substrate pattern in said first field of view comprising the steps of: a. transforming said pixel maps from said first and second fields of view using a two dimensional Fourier like transform to convert those pixel maps from the spatial domain to the frequency domain; b. identifying those frequencies in both dimensions having amplitude maxima in the frequency domain of step a. with the repeating pattern portions of each of said pixel maps from said first and second fields of view occurring at those frequencies in the frequency domain; c. entering zero values for the amplitudes at the frequencies in both dimensions identified in step b. to remove the amplitude at the harmonic frequency values of the repeating portions of said first and second fields of view; and d. inverse transforming the results from step c. using the inverse of the two dimensional Fourier like transformation of step a. to obtain modified spatial domain pixel maps of said first and second fields of view with the repeating patterns removed.