With increase in prices of food grains and non-renewable fuel, the scientific community has turned to nature for answers. Biomass and bio-fuel production system must be optimized to enhance bio-fuel production. This can be done with a bio-energy crop production system concentrating on farm profitability and resource energy management. The system defined here stands on climatic and geo-spatial characteristics of potential energy crops, production and availability of infrastructure, socioeconomic parameters, public (subsidies) as well as private fuel consumption, qualitative and quantitative analysis of bio-fuel crops, cultural guards and intrusions. This article presents a linear programming model considering the above parameters as inputs. The model seeks to accurately determine the profitability of each bio-fuel crop pair which can be rotated in a specific geography. Simulations to relate mean distance to bio-refinery and net biomass crop profit are performed for four region specific bio-fuel crop pairs in the United States. The model helps in understanding the connections that agricultural management is having with various parameters connected with production starting from cost of seeds to value of the final biomass in hand. This helps in the derivation of a stochastic model providing an insight on statistical impacts of multiple parameters on improving the feasibility of the proposed bio-fuel production system. This analysis implies closer bio-refinery spacing than current grain elevator spacing under most anticipated circumstances signifying that transportation infrastructure plays a significant, perhaps dominant, role in creating successful regional biofuel production programs and policies.