A method for removing undesirable contaminants from a chip passivation layer surface without creating SiO2 particles on the passivation layer, wherein the undesirable contaminants include graphitic layers and fluorinated layers. The use of N2 plasma with optimized plasma parameters can remove through etching both the graphitic and fluorinated organic layers. The best condition for the N2 plasma treatment is to use a relatively low-power within the range of 100-200 W and a relatively high vacuum pressure of N2 in the range of 500-750 mTorr.