In a pulmonary ventilation system, a filter arrangement useful as an input filter arrangement and an output filter arrangement is constructed to allow for changing or cleaning of the filter without interrupting or impacting the ventilation therapy and to limit the release of pathogens to the surrounding area or atmosphere. A preferred exhaust filter is constructed to function as a water trap and filter. Methods of operating the pulmonary ventilation system are also disclosed along with kits containing materials to construct an input or an output filtration structure.