Provided herein are isolation processes and the associated hardware to allow fluid streams to be isolated from a sterilized system (e.g., a sterile process vessel) that contains a sterile process. The isolation processes described herein allow for continuous removal of fluid streams (e.g., waste streams, liquid containing recombinant therapeutic proteins) from a sterilized system (e.g., a biological manufacturing system), which provides for less manual manipulation of the sterilized system and a decreased risk of contaminating the sterilized system.