To access the sugars in lignocellulosic biomass, pretreatment is an essential step to deconstruct the recalcitrant plant cell wall structures and facilitate enzymatic hydrolysis of recovered cellulose. Ionic liquid (IL) pretreatment is gaining substantial attention as a potential pretreatment process that can efficiently fractionate biomass and provide clean sugar substrate for the production of ethanol and other advanced biofuels. Previous work at Joint BioEnergy Institute (JBEI) has demonstrated at milliliter scales that IL can dissolve significant amounts of several feedstocks and produce highly digestible polysaccharides. However, a key factor in the development of economically viable lignocellulosic biofuels is to establish novel pretreatment technologies coupled with saccharification by advanced enzyme systems at process relevant scales.