This report describes the structure of the October 2012 version of the Biomass Scenario Model (BSM) in considerable detail, oriented towards readers with a background or interest in the underlying modeling structures. Readers seeking a less-detailed summary of the BSM may refer to Peterson (2013). BSM aims to provide a framework for exploring the potential contribution of biofuel technologies to the transportation energy supply for the United States over the next several decades. The model has evolved significantly from the prototype developed as part of the Role of Biomass in America" tm s Energy Future (RBAEF) project. BSM represents the supply chain surrounding conversion pathways for multiple fuel products, including ethanol, butanol, and infrastructure-compatible biofuels such as diesel, jet fuel, and gasoline.