An overlay metrology system is disclosed. The overlay metrology system includes a controller configured to be communicatively coupled with an overlay metrology subsystem. The controller receives overlay measurements from the overlay metrology subsystem and generates one or more quality metrics. The controller extracts a set of principle components from the one or more quality metrics. The controller generates input data and inputs the input data into an input matrix of a supervised machine learning algorithm to train a predictive model. The controller then identifies a recipe or hardware configuration with a minimum residual value.