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Millimeter-scale magnetic rotating swimmers have multiple potential medical applications. They could, for example, navigate inside the bloodstream of a patient toward an occlusion and remove it. Magnetic rotating swimmers have internal magnets and propeller fins with a helical shape. A rotating magnetic field applies torque on the swimmer and makes it rotate. The shape of the swimmer, combined with the rotational movement, generates a propulsive force. Visual feedback is suitable for in-vitro closed-loop control. However, in-vivo procedures will require different feedback modalities due to the opacity of the human body. In this paper, we provide new methods and tools that enable the 3D control of a magnetic swimmer using a 2D ultrasonography device attached to a robotic arm to sense the swimmer’s position. We also provide an algorithm that computes the placement of the robotic arm and a controller that keeps the swimmer within the ultrasound imaging slice. The position measurement and closed-loop control were tested experimentally.