A system for processing fluids and filling a container with a product includes a disposable fluid circuit and reusable hardware configured to accept the disposable fluid circuit. The disposable fluid circuit includes a spinning membrane separator, first and second syringes, and a flow control cassette. The reusable hardware includes a drive coupled to the spinning membrane separator, first and second syringe pumps, the first and second syringes coupled to the first and second syringe pumps respectively, and a controller. The system also includes a syringe pump for filling low-volume containers, which syringe pump may be one of the first and second syringe pumps, or may be a third syringe pump. The syringe pump for filling low-volume containers may include a filtered vacuum/pressure source and a position detector.