A global multiple-input multiple-output modal parameter scheme is employed with the frequency response function (FRF) matrix, to accurately estimate modal parameters of the closely coupled modes of a flexible disk-flexible shaft system from simulated data. The Lagrangian approach is combined with the assumed mode method to derive the governing equations of motion, where the uncoupled disk and shaft modes are employed as the assumed functions. The corresponding state space equations are obtained, which were integrated to provide response at points of interest (output, or response degrees of freedom) due to excitation at desired points (input, or excitation degrees of freedom). Random noise is added to the obtained time signal to simulate actual vibration measurements. The excitation and response time signals are used to generate the corresponding FRF matrix, used in the modal parameter estimation scheme. The extracted modal parameters are found to be in excellent agreement with theoretical results.