In this paper, position control and reduction of vibration of a 3D flexible L-shape mechanism has been achieved through the synthesis of a constrained Model Predictive Control (MPC). A finite element model, based on the equivalent rigid link system (ERLS) theory, is used in order to describe accurately the dynamic behaviour of the system. The model has been validated through the experimental tests. In order to apply the constrained MPC control on the mechanism, a linearized model which takes gravity force into account is derived as well as a Kalman state estimator. The effectiveness and robustness of the control system has been evaluated and discussed through several tests. Furthermore, the performance of the MPC control has been compared with the performance of classical industrial control (PID).