Biomass has the potential to create sustainable energy systems, which is critical for societal welfare. A major issue regarding biomass resources is crop residues or leftover biomass that is burnt by farmers after harvesting; this happens due to high transportation costs which make burning the cheapest way to remove the residue. We develop a decision support system using a large-scale linear program with the goal of maximizing profit with and without the emission cost. This system helps identify farms that would benefit society were they to be incentivized under a biomass crop assistance program (BCAP). A case study of leftover corn stover in the state of North Dakota is analyzed to validate the model. Our results reveal that an incentive of $7.20 per ton of corn stover converted to ethanol when 20% of rail capacity is allocated is ideal, as it produces the lowest emissions of 16,784,953 metric tons with a $73,462,599 profit. Furthermore, penalizing emissions resulting from the transportation of corn stover also helps reduce emissions; a suitable value for the penalty could be $71.7 per metric ton of CO2 emitted. Such a policy would result in reducing dependency on petroleum, thus promoting a sustainable biomass supply chain.