A method of calibrating a lithographic apparatus, the lithographic apparatus, comprising a support for a substrate a patterning subsystem for applying a pattern to the substrate, a measurement subsystem for measuring features on the substrate and a positioning subsystem for controlling the support and the patterning subsystem so as to apply the pattern at a desired position on the substrate, the accuracy of applying the pattern being dependent upon use of calibration data for correcting apparatus-specific deviations in the performance of the lithographic apparatus across the substrate, the method comprising:
- (a) providing a primary reference substrate having primary reference features positioned thereon, the positioning of the primary reference features being adopted as an accurate reference for calibration of the lithographic apparatus;
- (b) providing a secondary reference substrate having secondary reference features positioned thereon;
- (c) obtaining and storing an apparatus-independent fingerprint of the secondary reference substrate relative to the primary reference substrate;
- (d) calibrating the lithographic apparatus using the secondary reference substrate and the stored apparatus-independent fingerprint together as a reference;
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- (e) using the secondary reference substrate and the stored apparatus-independent fingerprint together as the reference to perform subsequent calibrations of the lithographic apparatus.