The design of biofuel processes is realised using a computer aided process system design methodology that aim at defining the type and the size of the technologies, the way they are interconnected and the way they are operated for a given socio-economical and environmental context. The method is using thermo-economic and environomic models of sub-systems that are structured in an equipment data base. In order to build the process, the equipment are assembled to build a flowsheet that represents the conversion of the raw materials (biomass) into products and by-products. Considering the different technological options to be used to build the flowsheet, a superstructure approach is used to systematically include all the possible combinations into a single process model from which the best flowsheet will be extracted using optimization techniques. In the process, energy is the driving force of the conversion. Therefore in the process design method, it is important to consider not only the mass flow interactions in the flowsheet but also the heat recovery and the combined heat and power production. The process integration is used to analyse, model and optimize the possible interactions between the equipments in the flowsheet. In the biofuel production processes, optimizing the process integration is of a major importance especially in thermo-chemical processes since the resource is also the energy source. Therefore increasing the efficiency of the energy conversion will at the sime time optimize the conversion efficiency of the raw material, maximizing the fuel production per unit of biomass. Several aspects of the process integration in biofuel production will be discussed and illustrated based on examples of synthetic natural gas and liquid fuels production from lignocellulosic biomass using thermo-chemical processes.