Input shaping is a low cost yet effective method for suppressing motion-induced vibration in point-to-point maneuverers. However, the success of shaper design largely depends on the accuracy of system dynamics, which are traditionally achieved by analytical dynamics. For systems with complex boundary conditions, motion constraints, and structural behaviors, such an approach could not yield effective models with sufficient accuracy. In this work, it is proposed to hire finite element dynamic simulation directly in both trajectory planning and input shaping design. Two flexible motion systems are designed for serving as the test bed to ensure multiple vibration mode excitations during transportation for evaluating the effectiveness in finite element simulation. Experimental results using both unshaped and shaped motions are performed. The associated finite element models are then simulated. The results confirm the effectiveness of using input shaping in vibration suppression and both the experimental and the simulation results agree to each other very well.