Provided is a method of determining, out of a plurality of shot regions of a substrate, a set of sample shot regions in each of which a position of a mark is to be actually measured. The method includes setting an initial arrangement of the set of sample shot regions, and adding, to the set of sample shot regions, a shot region, among the shot regions other than the sample shot regions in the initial arrangement, in which a value indicating uncertainty of an estimate of a measurement value of a position of a mark obtained using an estimation model exceeds a predetermined threshold value.