An apparatus for processing a biological sample for optical analysis having a cartridge with a sample supply container and a couvette, a cartridge/magazine holding the cartridge, and a cassette fan positioned over the cartridge. A filter cassette is mounted within the cassette fan, wherein the filter cassette has an inlet for receiving a sample from the sample supply container, an outlet for discharging the filter sample into the couvette, and valves therein to manipulate the sample for filtering. A cassette clamp is positioned over the filter cassette to secure the cassette and operate the filter cassette. A method for implementing this apparatus is also described herein. Additionally an apparatus is used for and a method measures waste fluid that passes over a filter element to control the amount of rinse fluid passing over the filter element.