Sensitivity calculations are provided of a process model through the rate of change of a model fingerprint with respect to process variables and defects. A fingerprint sensitivity table is generated, where process variables are associated with a set of fingerprint sensitivities. The fingerprint of incoming substrates is monitored through a production process by applying the same fingerprint method that is used in the process model. Calculations are made of the difference between the incoming substrate fingerprint and the process model predicted fingerprint. This difference fingerprint is compared against the table of fingerprint sensitivities to find the process variable most likely to be responsible for the difference. Spatial relationships between process variables and actual measurements on the substrate may be obtained. Correlation through fingerprint sensitivity improves the ability to pinpoint faulty process tools. The difference fingerprint may also identify the formation of defects on a substrate.