A method for determining substrate deformation includes obtaining first measurement data associated with mark positions, from measurements of a plurality of substrates; obtaining second measurement data associated with mark positions, from measurements of the plurality of substrates; determining a mapping between the first measurement data and the second measurement data; and decomposing the mapping, by calculating an eigenvalue decomposition for the mapping, to separately determine a first deformation (e.g. mark deformation) that scales differently from a second deformation (e.g. substrate deformation) in the mapping between the data. The steps of determining a mapping and decomposing the mapping may be performed together using non-linear optimization.