An apparatus for estimation of at least one parameter of interest of a feature fabricated on a substrate, the feature having a plurality of structure parameters, the structure parameters comprising the at least one parameter of interest and one or more nuisance parameters, the apparatus comprising:
- a receiver configured to receive radiation scattered from one or more measured features on the substrate;
- a pupil generator configured to generate an unprocessed pupil representation of the received radiation, the unprocessed pupil representation comprising a plurality of pixels each having an intensity indicative of the at least one parameter of interest and the one or more nuisance parameters;
- a matrix multiplier configured to multiply a transformation matrix with the intensities of each of the plurality of pixels of the unprocessed pupil representation to determine a post-processed pupil representation in which effects of the one or more nuisance parameters are mitigated or removed;
- and
- a parameter estimator configured to estimate the at least one parameter of interest based on the post-processed pupil representation.