A method is provided for reducing the amount of film fragments discharged into a processing liquid circulation system during removal of films from wafers, thereby reducing the frequency of filter cleaning or filter replacement. The method includes exposing a wafer containing a film formed thereon in a process chamber of a substrate processing system to a processing liquid, where the wafer is not rotated or is rotated at a first speed and the processing liquid is discharged from the process chamber to a processing liquid circulation system. Subsequently, exposure of the wafer to the processing liquid is discontinued and the wafer is rotated at a second speed greater than the first speed to centrifugally remove fragments of the film from the wafer. Next, the wafer is exposed to the same or a different processing liquid and the processing liquid is discharged from the process chamber to a processing liquid drain.