Frog-leg robots have been widely used for handling silicon wafers inside the vacuum environment of semiconductor manufacturing machines. In order to enhance stiffness, frog-leg robots adopt a parallel structure. A main challenge of controlling wafer handling robot is avoiding vibration, which is the major cause of wafer sliding and particle contamination. This paper presents two control approaches to improve the performance of frog-leg robots. First, in addition to the basic tri-loop PID feedback controller, torque offset is injected to the input of the robot to compensate the robot's nonlinear dynamics. This reduces the following error and major vibration. The torque offset is calculated based on identified robot dynamics. Second, a test based optimization method is developed to tune the gains of the feedback controller. Wafer vibration is measured and analyzed to score the system performance. Comparison results show that the proposed control scheme gives much improved performance.