NOVELTY - Method comprises e.g. (a) (i) providing biomass containing e.g. celluloses, (ii) removing sulfur compounds and nitrogen compounds from the biomass by contacting the biomass with a digestive solvent to form a pretreated biomass containing soluble carbohydrates, (iii) contacting the pretreated biomass 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.    USE - The method is useful for forming liquid fuel, preferably biodiesel.    ADVANTAGE - The method and system remove a substantial amount of nitrogen compounds, and sulfur compounds. The process provides increased conversion and conversion efficiency by minimizing catalyst poisoning and extending catalyst life. The method is cost-effective.    DETAILED DESCRIPTION - Method comprises: either (a) (i) providing a biomass containing celluloses, hemicelluloses, lignin, nitrogen, and sulfur compounds, (ii) removing sulfur compounds and nitrogen compounds from the biomass by contacting the biomass with a digestive solvent to form a pretreated biomass containing soluble carbohydrates and having less than 35% of the sulfur content and less than 35% of the nitrogen content based on untreated biomass on a dry mass basis, (iii) contacting the pretreated biomass 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; or (b) steps (i) and (ii), (vii) contacting at least a portion of the pretreated biomass with a recycle solvent stream to form a digested portion of the pulp, (viii) contacting at least a portion of the digested portion of the pulp with an aqueous reforming catalyst to form oxygenated intermediates, (ix) recycling a first portion of the oxygenated intermediates to form in part the recycle solvent in step (vii), and (x) processing at least a second portion of the oxygenated intermediates to form a liquid fuel; or (c) steps (i) and (ii), (xi) contacting at least a portion of the pretreated biomass with a recycle solvent stream to form a digested stream, (xii) contacting at least a portion of the digested portion of the digested stream directly with hydrogen in the presence of a hydrogeno lysis catalyst to form a first intermediate stream; (xiii) a first portion of the first intermediate stream is recycled to form in part the recycle solvent in step (xi), (xiv) contacting at least a portion of the first intermediate stream with an aqueous reforming catalyst to form an oxygenated intermediates stream, and (xv) processing at least a first portion of the oxygenated intermediates to form a liquid fuel. INDEPENDENT CLAIMS are included for a system comprising: a digester that receives a biomass feedstock and a digestive solvent operating under conditions to remove nitrogen compounds and sulfur compounds from the biomass feedstock and discharges a treated stream comprising a carbohydrate having less than 35% of the sulfur content and less than 35% of the nitrogen content based on untreated biomass feedstock on a dry mass basis, 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 digester as at least a portion of the digestive solvent, and a fuels processing reactor comprising a condensation catalyst that receives a second portion of the oxygenated intermediate stream and discharges a liquid fuel; and the digester, the aqueous phase reforming reactor, a first fuels processing reactor comprising a dehydrogenation catalyst that receives a second portion of the oxygenated intermediate stream and discharges an olefin-containing stream, and a second fuels processing reactor comprising an alkylation catalyst that receives the olefin-containing stream and discharges a liquid fuel.