A new method to identify the characteristic matrices from the response of the vibration system (transfer function) was proposed in the 1st report, and the accuracy of the proposed method was confirmed by the calculation using the transfer function without any experimental error. In this report, the characteristic matrices of a cantilever beam and a free-free beam are identified from the measured transfer function having some experimental error. When the transfer function containing sufficient information about the vibration system is used for identification, the characteristic matrices are accurately identified from the measured results containing some error, and the accuracy of the proposed method is confirmed again. Next the characteristic matrices of whole structure is derived by combining the experimentally or theoretically identified characteristic matrices of two sub-structures. The transfer function calculated using combined characteristic matrices of whole structure is a little different from the measured results. Because this difference is caused by the error in the identified characteristic matrices of the substructures, for the practical application of this estimating procedure the more accurate approach based on the proposed identification method must be developed.