Decreasing fossil fuel reserves and environmental concerns necessitate a shift toward biofuels. However, the chemistry of many biomass to fuel conversion pathways remains to be thoroughly studied. The future of biorefineries thus depends on developing new pathways while optimizing existing ones. Here, potential chemicals are added to create a superstructure, then an algorithm is run to enumerate every feasible reaction stoichiometry through a mixed integer linear program (MILP). An optimal chemical reaction pathway, taking into account thermodynamic, safety, and economic constraints is then found through reaction network flux analysis (RNFA). The RNFA is first formulated as a linear programming problem (LP) and later recast as an MILP in order to solve multiple alternate optima through integer cuts. A graphical method is also developed in order to show a shortcut method based on thermodynamics as opposed to the reaction stoichiometry enumeration and RNFA methods. A hypothetical case study, based on the conversion of woody biomass to liquid fuels, is presented at the end of the work along with a more detailed look at the glucose and xylose to 2-mthyltetrahydrofuran (MTHF) biofuel production pathway.