In the push for clean and renewable fuels, timber derived biomass is a promising frontier for biofuel production in the United States. This thesis approaches the established timberlands biofuel implementation problem with three different mathematical programming studies, each testing feasibility and sustainability in different economic and supply related situations. In the first study, a competitive game theory approach was utilized to provide new insights into the behavior within a timberlands supply chain. We utilized Stackelberg game theory modeled with bilevel programming to represent the competing harvesting and manufacturing sectors. In the second study, the initial bilevel model was utilized in a larger two stage multiperiod model with parameter uncertainty. In this more realistic model, the first stage contained logistical decisions around biorefinery investments, such as location and capacity, while the second stage was composed of multiple discrete bilevel scenarios representing potential situations in the timberlands system. The final study focused on long term land management strategies for the timberlands supply chain. Introduction of a new biorefinery investment meant that management strategies must be altered to ensure consistent material flows to manufacturers as well as sustain the new production facility. A modified cyclic scheduling formulation was used to model a timberlands system and its planting and harvesting schedule to accommodate a new biorefinery. This cyclic model added an initial startup period to initiate biofuel production and provide time to adapt land management. The overall contribution of these studies was to analyze a biorefinery's impact on the established behavior in a timberlands supply chain. In particular, the goals of these models were to develop introductory decision making tools for timberlands supply chain managers.