This dissertation is about the biomass supply chain network design considering the incentives as a financial support for entities in the supply chain such as the growers (farm) and biorefinery (plant) to produce energy (bioethanol) from the corn stover as a renewable energy feedstock. This dissertation consists of two journal papers that I have worked on during the past years of my Ph.D. studies where one of them has been published in Energy Policy journal. In the first paper, we presented a linear program (LP) model for the biomass supply chain network design in bioethanol production using corn stover. The distribution of the corn stover from farm to storage and plant, and the bioethanol from the plant to customer is modeled with the consideration of financial incentives. We explore the dollar value paid to the farmers to encourage them to convert the corn stover into bioethanol rather than burn it in the farm. Results show that only 37% of corn stover can be converted to bioethanol due to plant capacity limitation. In the second paper found in Chapter 3 in this dissertation, we presented a mixed integer linear program (MILP) model to overcome the plant capacity problem in the previous model. To make sure 100% corn stover converted to bioethanol, the MILP model will decide whether to expand the existing plant or build new plant based on existing plant configuration (EP) and combination of existing and new plant configuration (ENP). Results indicated that 100% corn stover converted to bioethanol can be achieved by expanding all existing plant and build a few new plants. It is also indicated that some farms are making losses in the EP configuration. Finally, we analyze the interaction of the farm and plant on the corn stover price and transportation cost to increase the profitability of the affected farms that are not making profit in the EP configuration.