This paper presents an efficient version of Hilbert-Huang transform for nonlinear non-stationary systems analyses. An ensemble empirical mode decomposition (EEMD) is introduced to alleviate the problem of mode mixing between intrinsic mode functions (IMFs) decomposed by EMD. Yet the problem has not been fully resolved when a signal of a similar scale resides in different IMF components. Instead of using a trial and error method to select the "best" outcome generated by EEMD, a hybrid algorithm based on EEMD and EMD is proposed for multi-mode signal processing. The developed approach comprises the steps from a bandpass filter design for regrouping modes of the IMFs obtained from EEMD, to the mode extraction using EMD, and to the assessment of each mode in the marginal spectrum. A simulated two-mode signal is tested to demonstrate the efficiency and robustness of the approach, showing average relative errors all equal to 1.46% for various noise levels added to the signal. The developed approach is also applied to a real bridge structure, showing more reliable results than the pure EMD. Discussions on the mode determination are offered to explain the connection between modegrouping form on the one hand, and mode-grouping performance on the other.