There is a growing need to find alternatives to crude oil as the primary feedstock for the chemicals and fuels industry. Ethanol has many desirable features as a petroleum substitute and could help smooth the transition from a petroleum-based to a bio-based economy. Among the various feedstocks for producing ethanol, corn stover and hybrid poplar (Populus nigra x Populus maximowiczii) interesting due to their wide availability in the US. Corn stover could be pretreated effectively using milder AFEX pretreatment conditions, while on the other hand poplar needs harsher AFEX conditions to obtain high sugar yields after enzymatic hydrolysis. Details of the pretreatment conditions and sugar yields with varying enzyme loadings will be discussed. We address subtle ultrastructure differences between corn stover and poplar and also reaction products generated during the AFEX process for both feed stocks. This research was performed within the Consortium for Applied Fundamentals and Innovation (CAFI2).