In recent years, Stewart platform manipulator (SPM) as a parallel manipulator, has drawn much attention among researchers and engineers in the area of robotics. Current applications of parallel manipulator include the motion base of simulators, the multi-axis vibration control of flexible structures and the vibration isolation of structures. The control system using dual processors, PC and DSP, is employed for the design of model based tracking control system of SPM, in which the feedback loop time of the DSP can be reduced to 1 msec, so that a model based controller with high speed feedback loop can be achieved. In order to reduce the control chattering, the relay function normally used in the conventional SMC is changed into a continuous function, which becomes a source of non-zero sliding function especially in the presence of a low frequency perturbation. The low frequency perturbation can be derived by utilizing the concept of time delay control and then a first order low-pass filter observer is additionally incorporated. It is shown numerically and experimentally that the proposed control system with the enhanced SMC guarantees the high speed motion control of the laboratory SPM under a high payload and the large virtual disturbance. The SPM is used for the multi-axis vibration control of the slender structure, using the concept of the flow source based vibration control to account the strong non-linearity and uncertainty of the SPM dynamics. In order not to cause the motion saturation of the actuator system, a hybrid dynamics associated with the flexible and desired SPM error dynamics is also modeled and redefined as the control object. It is experimentally shown that the two bending and one torsional coupled vibrations can be effectively controlled by the three rotational motions of the SPM regardless of the small model uncertainty of the flexible dynamic system without tracking error of SPM.