Methods are disclosed for measuring target structures formed by a lithographic process on a substrate. A grating structure within the target is smaller than an illumination spot and field of view of a measurement optical system. The optical system has a first branch leading to a pupil plane imaging sensor and a second branch leading to a substrate plane imaging sensor. A spatial light modulator is arranged in an intermediate pupil plane of the second branch of the optical system. The SLM imparts a programmable pattern of attenuation that may be used to correct for asymmetries between the first and second modes of illumination or imaging. By use of specific target designs and machine-learning processes, the attenuation patterns may also be programmed to act as filter functions, enhancing sensitivity to specific parameters of interest, such as focus.