A method is used to estimate a value representative for a level of alignment mark deformation on a processed substrate using an alignment system. The alignment sensor system is able to emit light at different measuring frequencies to reflect from an alignment mark on the substrate and to detect a diffraction pattern in the reflected light in order to measure an alignment position of the alignment mark. The two or more measuring frequencies are used to measure an alignment position deviation per alignment mark associated with each of the two or more measuring frequencies relative to an expected predetermined alignment position of the alignment mark. A value is determined representative for the spread in the determined alignment position deviations per alignment mark in order to estimate the level of alignment mark deformation.