In the measurement of properties of a wafer substrate, such as Critical Dimension or overlay a sampling plan is produced 2506 defined for measuring a property of a substrate, wherein the sampling plan comprises a plurality of sub-sampling plans. The sampling plan may be constrained to a predetermined fixed number of measurement points and is used 2508 to control an inspection apparatus to perform a plurality of measurements of the property of a plurality of substrates using different sub-sampling plans for respective substrates, optionally, the results are stacked 2510 to at least partially recompose the measurement results according to the sample plan.