Controlling a multiple-array, sheetmaking cross-directional process with a multivariable model predictive controller (MPC) employs a cost function incorporating a prediction horizon. The MPC provides a measurement profile target reference trajectory over the prediction horizon of the MPC cost function. Improved CD-MPC performance is achieved by employing a measurement profile target reference trajectory over the prediction horizon in the MPC cost function. A series of target profiles creates a reference trajectory to bring the cross-direction measurements smoothly from their current profile to the final target. By carefully designing the reference trajectory, the CD-MPC exhibits a good measurement response without aggressive control action. The current measurement target profile can be filtered through a first order plus deadtime process at each controller update and repeating the filter operation once for each step of the MPC prediction horizon generates a full reference trajectory for the profile.