A data analysis method and system are presented for use in determining one or more parameters of a patterned structure located on top of an underneath layered structure. According to this technique, input data is provided which includes first measured data PMD being a function ƒ of spectral intensity Iλ and phase φ, PMD=ƒ(Iλ;φ), corresponding to a complex spectral response of the underneath layered structure, and second measured data Smeas indicative of specular reflection spectral response of a sample formed by the patterned structure and the underneath layered structure. Also provided is a general function F describing a relation between a theoretical optical response Stheor of the sample and a modeled optical response Smodel of the patterned structure and the complex spectral response PMD of the underneath layered structure, such that Stheor=F(Smodel; PMD). The general function is then utilized for comparing the second measured data Smeas and the theoretical optical response Stheor, and determining parameter(s) of interest of the top structure.