The final functionality of parts produced by Additive Manufacturing (AM) can, in part, be improved by the inclusion of multi-material capabilities. The Multi3D Manufacturing System uses material extrusion printing (fused deposition modeling technology from Stratasys), solid conductor wire embedding, direct-write, component placement, and micromachining to enable the fabrication of multi-functional products. The material handling methodology, implemented by the Multi3D System, transports a workpiece between manufacturing stations via a six-axis robot, portable build platform, and a controlled temperature environment or chamber that travels to each manufacturing station. Also discussed in this work, is the investigation and improvement of registration parameters between the two material extrusion printers within this system. The registration was ultimately quantified to have minimal errors: 69μm along the x-axis, 183μm along the y-axis, and 215μm along the z-axis. The fabrication of a multi-colored part demonstrated the automated transfer of the workpiece, which offers early promise for an automated solution for multi-material fabrication using commercially-available fused deposition modeling machines.