Embodiments of the present invention overcome the well-known recalcitrance of lignocellulosic biomass in an economically viable manner. A process and a system are provided for the efficient fractionation of lignocellulosic biomass into cellulose, hemicellulose, and lignin. The cellulose and hemicellulose thus obtained are highly amorphous and can be readily converted into highly concentrated mixtures of five and six carbon sugars using known methods. Typical yields of sugars exceed 100 grams of sugars per liter of sugar solution. Other products, such as alcohols, can easily be prepared according to methods of the invention. The modest process conditions and low solvent/solid ratios of some embodiments of the invention require relatively low capital and processing costs.