A method for cleaning a fluidic system of a flow cytometer having a sheath pump to pump sheath fluid towards an interrogation zone and a waste pump to pump the sheath fluid and a sample fluid as waste fluid from the interrogation zone, wherein the sheath pump and/or the waste pump draw sample fluid into the flow cytometer through a drawtube towards the interrogation zone. The method includes controlling the sheath pump and the waste pump to cooperatively flush a fluid out through the drawtube, thereby cleaning the fluidic system of the flow cytometer.