In this research, we have proposed a methodology for experimental identification of modal parameters based on measurement of the frequency responses of structures with complex geometries and performed an overall investigation of structural behavior on a funnel-shaped inlet of magnetic resonance tomograph. Several identification methods are implemented and compared: complex exponential, least-squares complex exponential, and polyreference least-squares complex exponential. We have implemented the modal parameter identification methodology within our own graphical user interface supported by MATLAB to create an independent tool for modal analysis. The estimation methods are compared and the comparison results are summarized showing based on tabular representation and stabilization diagrams significant advantage of the proposed methodology for determining eigenfrequencies, damping coefficients, mode shapes, and residues for complex structures investigated in broad band of frequencies. Runtime for the execution of algorithms vary depending on the applied method, assumed order of the model used for estimation, and the number of measurements, that is, inputs and outputs.