Methods of optimizing a metrology process are disclosed. In one arrangement, measurement data from a plurality of applications of the metrology process to a first target on a substrate are obtained. Each application of the metrology process includes illuminating the first target with a radiation spot and detecting radiation redirected by the first target. The applications of the metrology process include applications at a) plural positions of the radiation spot relative to the first target, and/or b) plural focus heights of the radiation spot. The measurement data includes, for each application of the metrology process, a detected pupil representation of an optical characteristic of the redirected radiation in a pupil plane. The method includes determining an optimal alignment and/or an optimal focus height based on comparisons between the detected pupil representations in the measurement data and a reference pupil representation.