Transportation logistics are a critical factor in the optimization of biomass supply chains. A single 25 million gallon per year cellulosic ethanol biorefinery will require 18,500 semi loads of bales to be delivered to the plant. For a typical corn stover biomass supply chain, baled corn stover must be transported in two phases. The first phase is from the field to a storage site while the second is from the storage site to the biorefinery. All activities in-between these two points are connected and together they form the biomass supply chain. The goal of supply chain optimization is to minimize the total cost of these activities (transportation cost per unit, inventory cost per unit etc.) while satisfying the supply demands of a biorefinery. This paper will report on a recent analysis of production scale biomass transportation. Intensive GIS tracking and videocapture of the loading, securement, hauling, and unloading events of industrially produced large square bales of corn stover were collected and results were summarized. Specific results including; metrics for measuring supply chain efficiency, current capability of biomass supply chains, and sensitivity analysis to improvements in future supply chains will be presented. The outcomes of this work will help in forming more efficient biofuel production process and improve biofuel life cycle as well.