A method of collecting medical waste in a waste collection unit using a disposable manifold and filter assembly. The disposable manifold and filter assembly includes a manifold housing with a plurality of inlets, a neck extending from the manifold housing to define an outlet, and a filter basket disposed in the manifold housing. The method includes inserting the neck into the waste collection unit to direct the medical waste passing through the disposable manifold and filter assembly into the waste collection unit. Tubes are connected to the inlets of the manifold housing to provide a path for the medical waste to travel from a target site, e.g., a patient, to the manifold housing. A vacuum is drawn in the waste collection unit to pull the medical waste through the tubes and into the disposable manifold and filter assembly where the medical waste is processed/filtered in a plurality of stages.