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In this paper, the authors analyze the dynamics of a magnetic guiding system and derive its analytical model with full degrees of freedom (DOFs). Then, an adaptive controller which deals with unknown parameters is proposed to regulate the five DOFs in this system. The guiding system, including sensors and driver subsystems, has actually been implemented. Based on the experimental results, satisfactory performance including stiffness and resolution has been achieved. This validates the design of the system hardware and demonstrates the feasibility of the developed controller.