A final scrubber in the inert carrier gas flow path of an elemental analyzer includes a manifold with valves for selectively bypassing a quick disconnect final scrubber housing that includes a filter tube and sealed gas fittings. The housing includes alignment members and a latch for positioning and locking the housing onto and in sealed engagement with the instrument's manifold. A switch detects the presence of the housing, and a control circuit controls valves to direct the inert gas flow though the filter tube or bypass the filter tube when the housing is removed. With this system, the final scrubber can be removed and replaced quickly without the use of tools while the carrier gas continues to flow though the furnace without interruption. Also, the valves can be closed to allow for segmented leak detection of the instruments gas flow path.