Second generation biofuels offer the opportunity to mitigate emissions from the growing transportation sector while respecting the scarcity of arable land in agriculture. Biomass-to-liquid (BtL) concepts based on large-scale gasification are capable of using low-quality residual feedstock, such as wheat straw or forest residues, for the production of transportation fuels. However, large amounts of biomass feedstock are required to achieve the economic capacity of a synthesis plant. Depending on the steepness of the terrain and the role of feedstock owners, biomass potentials can only be utilized to a large extent at increasing costs per ton. Such diseconomies of scale are particularly problematic in the presence of already established value chains consuming the easily accessible and low-cost feedstock. As a result, second-generation biofuel supply chains face steep supply curves with sharply increasing unit costs. This article investigates the impact of established utilization paths on a large-scale biofuel production value chain. To do so, a mixed-integer linear model is presented which first determines the allocation of biomass resources to CHP plants and domestic consumers. Based on the resulting costs and supply curves, the model then determines the optimum configuration of the synfuel supply chain including locations and capacities of conversion plants, feedstock procurement and transportation. The model is applied to a case study covering six regions in south-central Chile. The total supply chain cost for the production of synthetic gasoline is estimated to amount to 0.8-0.9 (sic) per liter. Feedstock costs of the synfuel supply chain are 20-50% higher in comparison to the price paid by CHP plants and households. The results indicate that both torrefaction and fast pyrolysis can be applied beneficially to utilize remote biomass resources which are less in demand by established consumers.