This paper aims to develop a high-precision controller for a flexible link manipulator using polynomial reference, feedforward input, and feedback control. The control objective is to move the tip of the flexible link to a target position as quickly as possible without exciting its resonant modes. Upon a frequency response-based system identification, a frequency-domain feedback controller is designed for reference tracking. The controller includes a proportional-integral controller, a lead filter, and a set of notch filters to control the rigid body and the flexible link dynamics. A set of polynomial reference and feedforward input trajectories are then designed to improve the tracking performance and minimize residual vibrations. The conventional polynomial reference is generated based on the rigid body motion of the system. A revised polynomial reference generation method is then developed by adding flexible motions to the conventional reference. Simulations and experimental tests indicate significant improvements in the performance of the control system using the revised polynomial trajectories.