Deformation of a substrate due to one or more processing steps is determined by measuring substrate alignment data at lithographic processing steps before and after the one or more processing steps. Any abnormal pattern in the alignment data differential is identified by comparing the calculated alignment data differential with previous data accumulated in a database. By comparing the abnormal pattern with previously identified tool-specific patterns for alignment data differential, a processing step that introduces the abnormal pattern and/or the nature of the abnormal processing can be identified, and appropriate process control measures can be taken to rectify any anomaly in the identified processing step.