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This paper presents 2D feedback control and open loop 3D trajectories of heterogeneous chemically catalyzing Janus particles. Self-actuated particles have enormous implications for both in vivo and in vitro environments, which make them a diverse resource for a variety of medical and assembly applications. Janus particles, consisting of cobalt and platinum hemispheres, can self-propel in hydrogen peroxide solutions due to platinum’s catalyzation properties. These particles are directionally controlled using static magnetic fields produced from a triaxial approximate Helmholtz coil system. Since the magnetization direction of Janus particles is often heterogeneous, and thereby not consistent with the propulsion direction, this creates a unique opportunity to explore the motion effects of these particles under 2D feedback control and open loop 3D control. Using a modified closed loop controller, Janus particles with magnetization both closely aligned and greatly misaligned to the propulsion vectors, were instructed to perform complex trajectories. These trajectories were then compared between trials to measure both consistency and accuracy. The effects of increasing offset between the magnetization and propulsion vectors were also analyzed. The effects this heterogeneity had on 3D motion is also briefly discussed. It is our hope going forward to develop a 3D closed loop control system that can retroactively account for variations in the magnetization vector.