A method and system are presented for use in characterizing properties of an article having a structure comprising a multiplicity of sites comprising different periodic patterns, where method includes providing a theoretical model of prediction indicative of optical properties of different stacks defined by geometrical and material parameters of corresponding sites, said sites being common in at least one of geometrical parameter and material parameter; performing optical measurements on at least two different stacks of the article and generating optical measured data indicative of the geometrical parameters and material composition parameters for each of the measured stacks; processing the optical measured data, said processing comprising simultaneously fitting said optical measured data for the multiple measured stacks with said theoretical model and extracting said at least one common parameter, thereby enabling to characterize the properties of the multi-layer structure within the single article.