A model analysis method has been developed in the paper. The method estimates the modal parameters of multiple input-output systems, assesses their quality, and seperates structural modes form computation ones. The modal parameter extraction algorithm is the least squares method with a finite difference model relating input and output time data. The quality of the estimated system model can be assessed in narrow frequency bands by comparing the measured and model predicted responses in time domain with the aid of digital filters. Structural modes can be effectively separated from computational ones using the convergence factor which represents the pole convergence rate. The modal analysis method has been applied to simulated and experimental vibration data to evaluate its utility and limitations.