Systems and methods for removing deposit in an aftertreatment system for an engine are disclosed herein. The method comprises determining an amount of deposits accumulated in the aftertreatment system, determining combustion targets for the engine in response to determining the amount of deposits exceeds a deposit threshold, and modulating an air mass flow for the engine based on the determined combustion targets. The air mass flow can be modulated by changing the position of the wastegate or the geometry of the variable geometry turbine (VGT).