Biomass technologies have been inundated with new ideas and innovations the industrial world and the labs posing new challenges to chemical engineering. Individual bio-based paths, production of a single chemical product or fuel have gradually taken a significant position in markets. Given the plethora of degrees of freedom related to different feedstocks, paths and portfolio of products, the area seems to be chaotic. Opposing to the vast amount of options and possibilities, systems technology has on offer powerful methods to optimize designs and systematize improvements of biomass processing systems. Systematic screening leads to a holistic approach of the problem far from the applications that focus on individual processes or plants. This paper introduces a methodology to address the systematic integration of biorefineries supporting decisions for selection and the integration of processing paths. The implementation takes the form of a synthesis model that is generalized with process and intermediates as appropriate to the case. For the estimation of cost the method uses regression models based on the thermodynamics of the process. The investment cost is quickly and roughly calculated based on energy losses resulting from the difference of the Lower Heating Value (LHV) of the inlet and outlet flows of a process. The methodology is applied to 82 different chemistries that lead to the production of more than 80 intermediate and final products. The biomass is decomposed to three main streams of C5 sugars, C6 sugars and lignin. Those intermediates are the precursors for bio-based products and fuels such as polyamides, PVC, polypropylene, ethanol, aromatic polyols, resins, vanillin etc. that can be their petrochemical counterparts. The model produces a rank of products identifying the optimal integrated flows. The optimization model results to an optimal solution of coproduction of xylonic acid polyamide and lignin based castor oil. An impressive observation coming out from the results is that high market price of the product do not offer tops in the ranking lists. Several case studies are presented additionally to illustrate the wide framework of the methodology. The case studies concern the effect of the market demand and prices, the impact of the supply chain - transport cost, risk factors and LCA aspects.