A method of optimizing an apparatus for multi-stage processing of product units such as wafers, the method includes: receiving object data representing one or more parameters measured across the product units and associated with different stages of processing of the product units; and determining fingerprints of variation of the object data across the product units, the fingerprints being associated with different respective stages of processing of the product units. The fingerprints may be determined by decomposing the object data into components using principal component analysis for each different respective stage; analyzing commonality of the fingerprints through the different stages to produce commonality results; and optimizing an apparatus for processing product units based on the commonality results.