A system detects targets located within patterns. It operates in the pupil plane by filtering the received signal from the surrounding pattern. A method includes illuminating a target and a surrounding pattern with radiation, detecting the radiation reflected by the target and the surrounding pattern and forming a first set of data based on the detected radiation, removing portions of the first set of data which correspond to the target to form reduced data, interpolating the remaining portions of the reduced data over the removed portions to form product data, and subtracting the product data from the first set of data to form target data.