The present invention provides processes and systems for treating biomass and, e.g., making biofuels, such as bioethanol, from the biomass. More particularly, one process according to the present invention includes (a) inducing at least a first portion of a composition containing biomass and a working fluid to flow into a passage of a fluid processing apparatus, (b) injecting a high velocity transport fluid into the composition through a nozzle communicating with the passage of the fluid processing apparatus, whereby the transport fluid applies a shear force to the composition such that the working fluid is atomized and a vapor and droplet flow regime is formed downstream of the nozzle, (c) condensing the vapor and droplet flow regime, (d) transferring the composition to a first holding vessel, and (e) holding the composition in the first holding vessel at a first predetermined temperature for a first predetermined period of time, wherein a liquefaction enzyme is added to the composition prior to or during the process. Thereafter, the composition may be further processed to form a biofuel, such as, e.g., bioethanol.