Biomass supply chain and resource assessment seek to encourage the sustainable and cost-effective use of biomass energy. Biomass resource assessment includes estimating the required quantity of material, considering the constraints (i.e., environmental and technical), and evaluating the amount of recoverable material that can potentially be available for biomass energy use. Knowledge concerning the quantity and the type of biomass is essential because the success of bioenergy is critically dependent on having a large supply of low cost, high quality biomass which allows for the design of sustainable bioenergy chains and the appropriate selection of energy conversion technologies. Designing integrated and sustainable biomass supply chains that are highly efficient and cheaper allow bioenergy to be more competitive when compared to the energy generated from traditional sources. Herein, technological challenges for the developing and scaling up of integrated bioenergy/biofuels systems, improving bioconversion technologies to be more cost-effective, enhancing efforts for productivity of energy crops, establishing bioenergy/biofuels markets, and logistics are discussed. Furthermore, modeling and processing techniques for the bioconversion of biomass to bioenergy, planning for a self-sufficient bioenergy/biofuels chain, and a techno-economic evaluation of an integrated cost effective biomass to bioenergy supply chain are presented.