A metrology unit includes an integrated reference target with which an automated system check process is performed. The automated system check process includes measuring a feature on the reference target and determining if the measurement is within a desired specification for the metrology unit. When the metrology unit fails the automated system check, or if otherwise warranted, an automated diagnosis process may be performed using the same integrated reference target. The automated system check and automated diagnosis may be optimized based on correlations between parameters of the automated qualification and parameters of the automated diagnosis. Similarly, the measurement of a processed wafer may be optimized based on a correlation between parameters of the metrology of the processed wafer and parameters of the automated system check.