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In this paper, hardware integration and control design for a dual-axis linear stepper (Sawyer) motor are addressed. In particular, the Sawyer motor used in the Yaskawa/MotoMan manufacturing system which is utilized in various applications such as assembly, packaging, sorting, and probing, is considered. These motors are equipped with four optical sensors with a position resolution of 0.25 microns. We develop a detailed model of the motor for control validation and provide a comparison of two control designs, namely, a PD (or PID) and a robust adaptive nonlinear controller. To achieve high performance, a number of practical issues (such as delay/latency, finite sampling time, sensor noise, commutation rate, etc.) need to be considered. Effects of these factors are outlined and experimentally demonstrated. Both the considered controllers utilize knowledge of motor position and velocity in all axes. Current measurements are not required. Either numerical differentiation or a dynamic observer can be used to construct the velocity signals from the measured position data. The designed nonlinear controller provides practical stabilization of position tracking errors and achieves better overall performance. Adaptations are utilized so that no knowledge of the electromechanical system parameters is required. The proposed nonlinear controller is robust to load torques, friction, cogging forces, and other disturbances satisfying certain bounds. Furthermore, the controller corrects for the unintended yaw and achieves synchrony of the motor and rotor teeth. We have also observed that if the rotational motion is not corrected for, the performance is very poor for both controllers. This is also true in the case of delay/latency and higher rates of commutation.