In biaxial contouring control applications, the inherent structural flexibility of machines can lead to position discrepancies between the manipulator and actuator, and thus deteriorate the manufacturing performance, especially when the controller is designed without available end-effector side feedback. In this work, we focus on the end-effector contouring control problem for industrial machines with position-dependent flexibility to improve the contouring performance while eliminating the effect of mechanical vibration. A model for the widely used cantilever beam machine is developed to describe the dynamics of the end-effector by capturing the rotation and coupled dynamics between axes. The proposed model is validated through experiment and systematically reduced to switched linear time-invariant models for controller design. By adopting the extended state observer, the proposed control architecture decouples the dynamics between the X and Y-axis and simplifies the controller design process. The model predictive control method is utilised for improving the contouring performance while reducing mechanical vibration. The efficacy of the proposed control framework is demonstrated and validated on the designed high-fidelity model. Performance comparisons between the proposed approach with benchmark controllers are presented.INDEX TERMS Manufacturing, contouring control, motion control, vibration and noise control.