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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 μm. A detailed mathematical model of the motor is developed, and two control designs for position tracking, namely, a PD (or PID) controller and a robust adaptive nonlinear controller, are described along with experimental results. A number of practical issues (such as delay/latency, finite sampling time, sensor noise, commutation rate, and motor rotation) that must be addressed to achieve high performance are outlined and experimentally demonstrated. Both of 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 robust adaptive nonlinear controller provides practical stabilization of position tracking errors and utilizes adaptations so that no knowledge of the electromechanical system parameters is required. The controller is robust to load forces and load torque (i.e., disturbance torque in yaw axis), friction, and cogging forces. Furthermore, the controller corrects for the unintended yaw and achieves synchrony of the motor and rotor teeth.