The invention relates to detecting targets located within patterns. The invention operates in the pupil plane by filtering the fourier transform from the surrounding pattern. In particular the method includes performing a fourier transform on reflected radiation data to form fourier transform data; removing portions of the fourier transform data which correspond to the target to form reduced fourier transform data; interpolating the portions of the reduced fourier transform data which were removed, to form product fourier transform data; and subtracting the product fourier transform data from the fourier transform data.