A systematic approach for model updating using the modal identification results is proposed. Modal identification provides mode shapes for physical quantities (acceleration strain, etc.) measured in specific directions at the location of the sensors. Besides, model updating involves the use of the mode shapes related to the nodal degrees-of-freedom of the finite element analytic model. Consequently, the mode shapes obtained by modal identification and the mode shapes of the model updating process do not coincide even for the same mode. Therefore, a method constructing transform matrices that distinguish the cases where measurement is done by acceleration, velocity and displacement sensors and the case where measurement is done by strain sensors is proposed to remedy such disagreement between the mode shapes. The so-constructed transform matrices are then applied when the mode shape residual is used as objective function or for mode pairing in the model updating process. The feasibility of the proposed approach is verified by means of a numerical example in which the strain or acceleration of a simple beam is measured and a numerical example in which the strain of a bridge is measured. Using the proposed approach, it is possible to model the structure regardless of the position of the sensors and to select the location of the sensors independently from the model.