Model Reference Control is used to force a system to track the response of an assigned reference model, where the reference model is often designed to reflect the desired properties of the system. If a linear reference model is used, Model Reference Control has a linearizing effect for nonlinear plants, allowing it to be cascaded with linear controllers. Model Reference Control has been used to force nonlinear flexible systems to behave linearly such that input shaping can be used to limit residual vibration. However, when a system encounters saturation limits, the vibration limiting property of input shaping is degraded. This paper proposes Model Reference Control with an adaptive input shaping method to account for saturation by modifying the input shaper after saturation has been encountered. Simulations are presented to illustrate the effectiveness of this method in canceling residual vibration for a nonlinear electromagnetic actuator subject to input constraints.