An apparatus and a method for filtering sectioning wastes of a microtome that are present in an air stream are described. The apparatus has an aspiration device with which sectioning waste can be aspirated from a blade region of the microtome with an air stream. A main filter and a prefilter are provided. A valve is provided for opening and closing an opening so that the air stream so that if desired an air stream can be directed through a filter insert in the prefilter for emptying the prefilter into the main filter. According to the method, an air stream that is used for aspirating sectioning waste from a blade region of the microtome is shut off immediately before emptying the prefilter.