The paper reports on the development of a direct flutter-onset prediction framework, based on CFD frequency-domain techniques, for a robust and efficient search of the flutter boundary across the flight envelope. The implementation was carried out in the open-source SU2 solver. The complete methodology is examined in this contribution. The existing harmonic balance formulation was extended to treat arbitrarily deforming surfaces. A dedicated native solver was developed to integrate the linear structural equations of motion. Reduced order structural equations are built based on input modal shapes from external FE solvers. To this end, suitable interpolation schemes have been included to transfer data across the fluid-structure interface. This paper provides numerical results from the application of the developed approach to wellestablished 2D and 3D test cases operating in the transonic regime. The accuracy of the chosen strategy is shown, and the robustness and computational efficiency of the implementation are discussed.