The goal was to develop a biomass conversion process that optimizes fractionation and conversion to maximize Carbon efficiency and Hydrogen consumption to obtain drop-in fuels. Selective fractionation of raw biomass was obtained via multi-stage thermal fractionation to produce different streams that are enriched in a particular chemical family (acids, furanics or phenolics). These streams were later catalytically upgraded in both liquid and vapor phase to perform C-C bond formation and hydrodeoxygenation. Among various upgrading strategies investigated we have identified an effective path in which cyclopentanone is a crucial intermediate that can be derived from furfural and other furanics obtained in high concentrations from this thermal staged process. Cyclopentanone is a very versatile molecule, which can couple with itself to product high quality jet-fuel, or couple with phenolic or furanics to create long chain molecules. These (mono-oxygenated) compounds in the correct molecular weight fuel range can be hydrotreated to direct drop-in fuels. Interestingly, we have found that the conversion of furfural to cyclopentanone is not affected by the presence of acetic acid, and, more interestingly, it is enhanced by the presence of water. These are very significant findings, since water and acetic acid are always present in all streams from the primary conversion stage. These results have allowed to complete detailed life-cycle assessment and techno-economic analysis that have been back-fed to the experimentalists to refine the catalyst selection and process operations with the objective of maximizing C efficiency at minimum H utilization. These combined investigations have opened the possibility of an economically and technologically effective process that could result in commercial fuels produced from renewable sources at a cost that might be competitive with fossil fuels.