A method of characterizing a deformation of a plurality of substrates is described. The method includes: measuring, for a plurality of n different alignment measurement parameters λ and for a plurality of substrates, a position of the alignment marks; determining a positional deviation as the difference between the n alignment mark position measurements and a nominal alignment mark position; grouping the positional deviations into data sets; determining an average data set; subtracting the average data set from the data sets to obtain a plurality of variable data sets; performing a blind source separation method on the variable data sets, thereby decomposing the variable data sets into a set of eigenwafers representing principal components of the variable data sets; and subdividing the set of eigenwafers into a set of mark deformation eigenwafers and a set of substrate deformation eigenwafers.