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This paper first reveals that the tracking and disturbance rejection problems can be decoupled into two independent optimization problems under the 2-DOF control framework. This result is then used for the design of a 2-DOF controller for a dual-stage actuator (DSA) system to provide desired performance of disturbance rejection and step tracking. The 2-DOF controller is designed based on the doubly coprime factorization approach, with which the closed-loop transfer function is expressed explicitly in terms of design parameters. This greatly simplifies the optimization of design parameters in meeting desired specifications. We further study how to use the design parameters to deal with specific problems in the DSA, i.e., control allocation and trajectory planning. For step tracking beyond the secondary actuator range, a nonlinear controller is also used for the primary actuator to complete the task. Experimental results demonstrate the practical implementation of the DSA control system and verify its effectiveness for step tracking and disturbance rejection and its robust performance under load changes.