Separations account for 60-80% of the processing costs of most mature chemical processes. Membrane based separations offer several advantages over conventional technology such as lower energy costs and easy scale up. Here we focus on membrane extraction for removal of acetic acid, sulfuric acid, furfural, HMF and other toxic compounds from biomass hydrolysates. As membrane extraction is non-dispersive it overcomes the disadvantages of conventional extraction. Experiments have been conducted using dilute sulfuric acid pretreated corn stover (hydrolysate). Acetic acid, in its protonated form, is extracted into an organic phase consisting of octanol/oleyl alcohol and Alamine 336, a tertiary amine, containing aliphatic chains of 8-10 carbon atoms. Co-extraction of sulfuric acid leads to an increase in hydrolyste pH. The effect of aqueous and organic phase flow rates and temperature, on the rate of extraction of acetic acid and sulfuric acid has been investigated. Changes in the rates of acetic and sulfuric acid extraction may be explained by considering the structure of the complexes formed in the organic phase. We conducted computational modeling to elucidate the extraction process of Alamine 336 in different solvents. Extraction of carboxylic acids, Furfural and HMF in water and octanol was simulated using the Gaussian 03 package. In the past the extraction process has been explained by the direct interaction of the carboxylic acid with the Alamine 336 to form an ion pair. More carboxylic acids could be extracted through hydrogen bonding forming a dimer or trimer complex form with the Alamine 336, stabilized by the organic solvent. Hydrolysates treated by membrane extraction and conventional conditioning technologies were fermented using a glucose-xylose fermenting bacteria to determine the viability of membrane technology to detoxify biomass hydrolysates. Membrane extraction could be a viable hydrolysate detoxification technology because the other conditioning technologies do not remove acetic acid.