NOVELTY - Producing biofuels from biomass involves: contacting biomass containing celluloses, hemicelluloses and lignin, with an aqueous media; separating at least a portion of an aqueous liquor; contacting aqueous liquor stream with a purification substrate effective to remove sulfur compounds and nitrogen compounds; contacting treated carbohydrate stream with an aqueous phase reforming catalyst to form oxygenated intermediates; and processing a portion of the oxygenated intermediates to form a liquid fuel.    USE - For producing biofuels from biomass, (claimed) which is used in transportation fuels such as synthetic gasoline, diesel fuel, and jet fuel and industrial chemicals.    ADVANTAGE - The methods and systems have an advantage of pretreating a raw biomass feedstock with an aqueous media to produce an aqueous liquor stream containing soluble carbohydrates that are further treated to remove nitrogen compounds and sulfur compounds and optionally phosphorus compounds contained in the biomass that tend to poison the catalysts prior to aqueous reforming processing. The treated biomass is then converted by aqueous phase reforming reactions to form an oxygenated intermediate stream comprising polyols, alcohols, ketones, aldehydes, and other oxygenated reaction products that can be fed directly to a processing reaction to form higher hydrocarbons, which results in an increased conversion and conversion efficiency by minimizing catalyst poisoning and extend the catalyst life. At least a portion of oxygenated intermediates produced in the aqueous phase reforming (APR) reaction are recycled within the process. This recycle saves costs and can increase the amount of carbohydrates extracted from the biomass feedstock. Further, by controlling the degradation of carbohydrate in the APR process, the hydrogenation reaction can be conducted along with the APR reaction at 175-275 degrees C. As a result, a separate hydrogenation reaction can be avoided and the fuel forming potential of the biomass feedstock fed to the process can be increased. This process also results in a capital cost savings and process operational cost savings.    DETAILED DESCRIPTION - Producing biofuels from biomass involves: (i) providing a biomass containing celluloses, hemicelluloses and lignin; (ii) contacting the biomass with an aqueous media to form an extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin; (iii) separating at least a portion of an aqueous liquor from the extracted biomass thereby providing the aqueous liquor stream comprising soluble carbohydrates and an extracted biomass solids stream comprising celluloses, hemicelluloses, and lignin; (iv) contacting the aqueous liquor stream with a purification substrate effective to remove sulfur compounds and nitrogen compounds thereby producing a treated carbohydrate stream having less than 35% of the sulfur content and less than 35% of the nitrogen content of the untreated aqueous liquor feed, based on the untreated aqueous liquor stream; (v) contacting the treated carbohydrate stream with an aqueous phase reforming catalyst to form oxygenated intermediates; and (vi) processing at least a portion of the oxygenated intermediates to form a liquid fuel. An INDEPENDENT CLAIM is included for a system comprising: a vessel that receives a biomass feedstock and an aqueous media operating under conditions effective to produce an extracted biomass comprising celluloses, hemicelluloses, soluble carbohydrates and lignin and discharges an aqueous liquor stream comprising soluble carbohydrates; a soluble carbohydrate treater comprising a purification substrate that receives the aqueous liquor and discharges a treated carbohydrate stream having less than 35% of the sulfur content and less than 35% of the nitrogen content of the untreated aqueous liquor feed; an aqueous phase reforming reactor comprising an aqueous phase reforming catalyst that receives the treated stream and discharges an oxygenated intermediate stream, where a first portion of the oxygenated intermediate stream is recycled to the vessel as at least a portion of the aqueous media; and fuel processing reactor comprising a condensation catalyst that receives a second portion of the oxygenated intermediate stream and discharges a liquid fuel.