A control system is presented for use in measuring one or more parameters of a three-dimensional patterned structure. The control system is configured as a computer system comprising a data processor configured to receive and process raw measured TEM image data, TEMmeas, and generate output data indicative of one or more parameters of a patterned structure. The data processor comprises an optimization module configured and operable to utilize data indicative of one or more parameters of TEM measurement mode and perform a fitting procedure between the raw measured TEM image data, TEMmeas, and a predetermined simulated TEM image data, TEMsimui based on a parametrized three-dimensional model of features of the patterned structure, and generate simulated image data corresponding to a best fit condition, to thereby enable determination therefrom of the one or more parameters of the structure.