A high-throughput system for processing biological material that comprises: a tray that supports a functionally-closed fluid path subsystem comprising, a vessel for containing and enabling the biological material to separate into two or more distinct submaterials; one or more receptacles to receive one or more of the submaterials from the vessel; a filtration device; a conduit through which one or more submaterials are transported between at least the vessel and the filtration device; and a first engagement structure; a processing unit comprising, a pumping device for moving one or more of the submaterials between at least the vessel and the filtration device via the conduit; a second engagement structure corresponding to the first engagement structure; a locking mechanism for at least temporarily holding the tray in a fixed position relative to the processing unit; a control device that automatically starts and stops the pumping device in response to one or more commands.