This paper analyzes the impact that an intermodal facility has on location and transportation decisions for biofuel production plants. Location decisions impact the management of the in bound and out-bound logistics of a plant. We model this supply chain design and management problem as a mixed integer program. Input data for this model are location of intermodal facilities and available transportation modes; cost and cargo capacity for each transportation mode; geographical distribution of biomass feedstock, and production yields; and biomass processing, and inventory costs. Outputs from this model are the number, location and capacity of biofuel production plants. For each plant, the transportation mode used, timing of shipments, shipments size, inventory size, and production schedule that minimize the delivery cost of biofuel are determined. The model proposed in this research can be used as a decision making tool for investors in the biofuels industry as it estimates the real cost of the business. The state of Mississippi is considered as the testing grounds for our model.