A method and system are presented for use in model-based optical measurements in patterned structures. The method comprises: selecting an optimal optical model for interpretation of optical measured data indicative of optical response of the structure under measurements. The selection of the optimal optical model comprises: creating a complete optical model with floating parameters defining multiple configurations of said complete model including one or more model configurations describing an optical response of the structure under measurements, utilizing the complete model for predicting a reference optical response from the structure and generating corresponding virtual reference data, and using the virtual reference data for selecting the optimal optical model for interpretation of the optical measured data.