Pretreatment processes have been identified as one of the significant cost prohibitive and inefficient steps to the development of cellulosic feedstock based fermentations in order to produce liquid fuels.  Previous research has emphasized the need for individual feedstock process optimization, typically specific to pretreatment methods.  More recent work has extended pretreatment to inlcude more efficient and complementary coupled methods.  With the use of SuperPro Designer, we have evaluated and performed mass and energy balances for coupled pretreatment pilot plant designs.  We highlight some of our experiences while using SuperPro Designer and present comparisons of varied pretreatment designs for fermentations used to produce liquid fuels.