A clean sequential process including clean fractionation and hydrothermal post-treatment was developed to fractionate and pretreat prairie cord grass (PCG) prior to ethanol fermentation. An optimized clean fractionation was applied to extract lignin; then, the remaining material was subjected to a hydrothermal treatment process to enhance cellulose digestibility. The main purpose of the hydrothermal post-treatment was to improve digestibility of delignified cellulose and reduce harshness of the clean fractionation process. Optimization was performed for solvent compositions as well as time and temperatures applied to each sequential process. The glucose yield was 89% from enzymatic hydrolysis and 92% from combined fractionation and hydrothermal treatments of PCG.