The objective of this thesis is to include strategic and tactical level decisions into the biorefinery supply chain design for a specific region while comparing multiple conversion technologies and biomass feedstocks. The allocation of biomass feedstocks, products, and the respective supply chain configuration locations are determined while ensuring the regions monthly biomass availability and product market demand constraints are met. This research considers all actions required to bring the bio-based products to market from harvesting, storing, and processing the biomass to market distribution. Two different conversion technologies are chosen for comparison: one advanced conversion technology and one conventional technology. Potential investors and policy makers will be able to use this region specific tool by maximizing annual profitability to evaluate potential lignocellulosic biomass feedstocks and conversion technologies for the production of energy, fuels, and chemicals. The tool utilizes ILOG OPL software for optimization while interfacing with Microsoft Excel for parameter inputs and results output. From the sensitivity analysis, further insight is gained to what key drivers greatly influence the performance of each supply chain. The results demonstrate the practicality of this tool, which then can be further analyzed through other models such as discrete event simulation.