Clean rooms are categorized into classes based on the number and size of particles permited per volume of air.  The number of HEPA filters on your clean room will help to determine the classification of the clean room.  HEPA filters actually filter air before it is presented to the clean room.  The clean air is then recirculated through and out of the room, allowing for particles generated within the room to be pushed out as well.  HEPA filters are quoted separately from the clean room assemblies.