An integrated instrument processes fluid test samples using disposable test devices. The test devices are carried in a carrier. The instrument includes a vacuum station receiving the carrier for batch loading of the test devices with fluid samples to be tested. The user removes the carrier from the vacuum station and inserts it into a loading station of a separate carrier and test device processing subsystem. This subsystem includes a transport system moving the carrier through the instrument where various modules perform operations on the test devices, including sealing the test devices, loading the test devices into an incubation station, incubation of the test devices, test device reading, and test device disposal.