Measurements are obtained from locations across a substrate before or after performing a lithographic process step. Examples of such measurements include alignment measurements made prior to applying a pattern to the substrate, and measurements of a performance parameter such as overlay, after a pattern has been applied. A set of measurement locations is selected from among all possible measurement locations. At least a subset of the selected measurement locations are selected dynamically, in response to measurements obtained using a preliminary selection of measurement locations. Preliminary measurements of height can be used to select measurement locations for alignment. In another aspect, outlier measurements are detected based on supplementary data such as height measurements or historic data.