In this paper, we review the current effort toward the design of production processes from different sources of biomass including first, second, and third generation of biofuels such as bioethanol, biodiesel, hydrogen, and FT-diesel. We review results of the design of these processes using mathematical programming techniques to systematically evaluate a large number of alternative technologies, by optimally integrating the use of raw material, energy, and water in order for the process not only to be economically feasible but also sustainable. Integration of processes is the future of biorefineries to exploit synergies that reduce the production cost.