This paper presents a comprehensive approach for the linearized frequency-domain analysis of hydrodynamic loading and structural responses on a deformable body. The structural and hydrodynamic analyses are integrated by employing the mode superposition method. Commencing with an eigenvalue analysis on the structural model, the shapes of selected modes, mass, and structural stiffness matrices are extracted as input to the subsequent hydrodynamic analysis, where the global response is solved in the modal space. The resulting hydrodynamic and inertial loads are then transferred to the same finite element model for stress assessment. To exemplify the proposed methodology, a bottom-fixed flexible cylindrical monopile and a long box-shaped barge model are investigated. For the barge model, the sectional loads are obtained from the integral of stresses in the cuts along the structure model, which are found to be consistent with those from the hydrodynamic analysis, demonstrating the consistency of the entire workflow. In particular, this paper introduces a straightforward formulation for evaluating the generalized restoring matrices, eliminating the need for spatial derivatives of the mode shape function and thereby significantly reducing numerical uncertainties in using the flexible modes derived from finite element model for hydrodynamic analysis.