This work investigates an additive manufacturing process, micro-Robotic Deposition (μRD), and its utility in fabricating advanced architecture synthetic bone grafts. The objective of this research is to develop a method to integrate different regions with different porous microstructures into a single scaffold; there is evidence that scaffolds with designed regions of specific microstructures can be used to elicit a strong and directed bone ingrowth response that improves bone ingrowth rate and quality. The key contribution of this work is integration of a control algorithm that precisely places different build materials in specified locations with a workflow that enables near-net shape fabrication, thereby the fabrication of advanced architecture scaffolds is feasible. Under previous control methods, designs were relegated to be composed of a single material with simple contours. Scaffolds with contoured forms, multiple domains with distinct porous microstructures, and hollow cavities are feasible when the developed controller is used in conjunction with a novel manufacturing workflow in which scaffolds are filled within patterned molds that support overhanging features.