A dual-hopper feed system that was developed for the Big Area Additive Manufacturing (BAAM) system allows for transitioning between different materials while maintaining continuous deposition. This technique creates a step-change in material feedstock by switching the pellet feeding system to alternate which hopper is currently supplying material, allowing for multi-material construction. The step-change in feedstock material produces a transition region that is characterized by a compositional gradient and blended internal morphology. Initial cross-sectional imaging of the transition region revealed a non-homogenous blend of materials with distinct domains of each material, likely due to incomplete mixing within the screw. This study used a carbon fiber reinforced acrylonitrile butadiene styrene (CF-ABS) and an unfilled ABS to characterize the internal structure and to correlate it to mechanical performance by tracking microhardness across cross-sections of the transition region.