Ultrasonic based inspection of thin-walled structures often requires prior knowledge of their mechanical properties. Their accurate estimation could be achieved in a non-destructive manner employing, e.g., elastic guided waves. Such procedures require efficient approaches for experimental data extraction and processing, which is still a challenging task. An advanced automated technique for material properties identification of an elastic waveguide is proposed in this investigation. It relies on the information on dispersion characteristics of guided waves, which are extracted by applying the matrix pencil method to the measurements obtained via laser Doppler vibrometry. Two objective functions have been successfully tested, and the advantages of both approaches are discussed (accuracy vs computational costs). The numerical analysis employing the synthetic data generated via the mathematical model as well as experimental data shows that both approaches are stable and accurate. The influence of the presence of various modes in the extracted data is investigated. One can conclude that the influence of the corruptions related to the extraction of dispersion curves is not critical if the majority of guided waves propagating in the considered frequency range are presented. Possible extensions of the proposed technique for damaged and multi-layered structures are also discussed.