Methods and systems for controlling motion of and optically tracking a mechanically unattached probe (202) in three-dimensions are disclosed. A mechanically unattached magnetic probe (202) is placed in the system under test. The position of the probe is optically tracked in three dimensions by sensing light scattered by the probe and direct light from a light source. Magnetic poles (200) positioned about the probe are selectively magnetized to control motion of the probe in three dimensions by minimizing error between a sensed position and a desired position. In one implementation, the coil currents are time division multiplexed such that the average force on the probe produces motion in a desired direction.