A flux residue cleaning system includes first and second immersion chambers, first and second spray chambers, and a drying chamber. The first immersion chamber softens an outer region of a flux residue formed around microbumps interposed between a wafer and a die when the wafer is immersed in a first chemical. The first spray chamber removes the outer region of the flux residue when the wafer is impinged upon by a first chemical spray in order to expose an inner region of the flux residue. The second immersion chamber softens the inner region of the flux residue when the wafer is immersed in a second chemical. The second spray chamber removes the inner region of the flux residue when the wafer is impinged upon by a second chemical spray in order to clean the wafer to a predetermined standard. The drying chamber dries the wafer.