A method and system for processing biomass. The method uses an apparatus with a housing, a rotor inside of the housing, and a plurality of protrusions extending from the rotor. The method includes placing the biomass in a fluid medium, inducing cavitation within the fluid to partially separate the biomass, sending the biomass and fluid into the housing, rotating the rotor to further separate the biomass, heating the biomass and fluid, and maintaining the acidity of the fluid and biomass at a pH of between approximately 2 to 6. The system includes apparatus each having a housing and a rotor within the housing. One apparatus has abutting, alternating height protrusions extending from the rotor. Another apparatus has grooves formed in the rotor and an end wall of the housing. Another apparatus has two rows of protrusions extending from the rotor that are spaced apart no less than approximately 6 millimeters.