A method to determine the usefulness of an alignment mark of a first pattern in transferring a second pattern to a substrate relative to the first pattern already present on the substrate includes measuring the position of the alignment mark, modeling the position of the alignment mark, determining the model error between measured and modeled position, measuring a corresponding overlay error between first and second pattern and comparing the model error with the overlay error to determine the usefulness of the alignment mark. Subsequently this information can be used when processing next substrates thereby improving the overlay for these substrates. A lithographic apparatus and/or overlay measurement system may be operated in accordance with the method.