Based on the HHT (Hilbert-Huang Transform), the ChebyshevⅠtype filter was adopted to process the measured free vibration signal to solve the mode-mixing problem, so that all the structural modes could be acquired from IMFs. Meanwhile, removing endpoints were used during the linear least-square fit procedure to avoid the endpoint effect. Besides obtaining the modal frequencies and damping ratios, the formulation of mode shapes of proportional-damping structure was also derived. The simulation results of 4-NDOF numerical case and 4-NDOF frame structure in the laboratory have demonstrated that the proposed approach is accurate and effective.