A storage container for autoclaving and storage of a medical instrument cassette includes a tray portion and a lid assembly which are securely closed together by means of a pair of spring-biased end latches. The lid assembly includes a lid gasket which is compressed by an outer lip of the tray portion and further includes a pair of low profile filter assemblies. Each filter assembly includes a retainer plate with an assembled edge seal, a paper filter, and a cover plate. The stack of these components creates a low profile design whose overall thickness in a direction normal to the surface of the lid is less than 3/8 of an inch. The cover plate is easily attached and removed for replacing the paper filter by means of keyhole-shaped apertures in the cover plate and lock studs assembled to the lid assembly which fit within the keyhole-shaped apertures. The two latch assemblies provide a visual indication as to whether the lid assembly is securely sealed onto the tray portion or is open.