Systems and methods are provided, which calculate overlay misregistration error estimations from analyzed measurements of each ROI (region of interest) in at least one metrology imaging target, and incorporate the calculated overlay misregistration error estimations in a corresponding estimation of overlay misregistration. Disclosed embodiments provide a graduated and weighted analysis of target quality which may be integrated in a continuous manner into the metrology measurement processes, and moreover evaluates target quality in terms of overlay misregistration, which forms a common basis for evaluation of errors from different sources, such as characteristics of production steps, measurement parameters and target characteristics. Such common basis then enables any of combining various error sources to give a single number associated with measurement fidelity, analyzing various errors at wafer, lot and process levels, and/or to trade-off the resulting accuracy for throughput by reducing the number of measurements, in a controlled manner.