A method including determining a position of a first pattern in each of a plurality of target portions on a substrate, based on a fitted mathematical model, wherein the first pattern includes at least one alignment mark, wherein the mathematical model is fitted to a plurality of alignment mark displacements (dx, dy) for the alignment marks in the target portions, and wherein the alignment mark displacements are a difference between a respective nominal position of the alignment mark and measured position of the alignment mark; and transferring a second pattern onto each of the target portions, using the determined position of the first pattern in each of the plurality of target portions, wherein the mathematical model includes polynomials Z1 and Z2: Z1=r2 cos(2θ) and Z2=r2 sin(2θ) in polar coordinates (r, θ) or Z1=x2−y2 and Z2=xy in Cartesian coordinates (x, y).