A method for controlling a boom assembly includes providing a boom assembly having an end effortor. The boom assembly includes an actuator in fluid communication with a flow control valve. A desired coordinate of the end effector of the boom assembly is converted from Cartesian space to actuator space. A deflection error of the end effector based on a measured displacement of the actuator is calculated. A resultant desired coordinate of the end effector is calculated based on the desired coordinate and the deflection error. A control signal for the flow control valve is generated based on the resultant desired coordinate and the measured displacement of the actuator. The control signal is shaped to reduce vibration of the boom assembly. The shaped control signal is transmitted to the flow control valve.