Ethanol production from lignocellulosic residues has potential to significantly improve sustainability of biofuels for transport by avoiding land-use competition with food crops and reducing impacts related to agricultural inputs. However, high production costs remain bottleneck for large-scale development of this pathway. A huge potential exists in upgrading energy producing pathways into biorefineries in order to improve its economic performance and long-term sustainability. A promising general model for a lignocellulosic biochemical refineries (LCBR) is based on sugar-lignin platform, in which 5-carbon (C5) and 6-carbon (C6) sugars, resulting from lignocellulosic matrix fractionation, are converted into fuels and building block chemicals by biotechnological or chemical pathways. In this context, comprehensive, flexible and dynamic modelling approaches are needed to solve a problem with multiple optimization criteria (economic and environmental), high levels of uncertainty and dynamic behaviour. Process simulators and comprehensive databases of production processes can help to determine rigorous and thermodynamically consistent material and energy balances permitting robust scale-up and reducing uncertainty in economical and environmental impact evaluation in a dynamic context. This paper discusses the need for developing a modular platform for process synthesis aiming at selection of technically, economically and environmentally sound pathways for lignocellulosic biorefineries.