Ultrasonic flip-chip bonding needs a precise bonding tool which delivers ultrasonic energy into chip bumps effectively to use the selected resonance mode and frequency of the horn structure. The bonding tool is excited at the resonance frequency and the input and output ports should locate at the anti-nodal points of the resonance mode. In this study, we propose new design method with topology optimization for ultrasonic bonding tools. The SIMP(solid isotropic material with penalization) method is used to formulate topology optimization and OC(optimal criteria) algorithm is adopted for the update scheme. MAC(modal assurance criterion) tracking is used for the target frequency and mode. We fabricate two prototypes of ultrasonic tools which are based on 3D optimization models after reviewing 2D and 3D topology optimization results. The prototypes are satisfied with the ultrasonic frequency and vibration amplitude as the ultrasonic bonding tools.