A method of removing non-polar colorants of a color filter array rapidly from a bottom layer starts by performing a cracking process to decompose cross-linked polymeric molecules of non-polar R/G/B colorants to smaller fragments. A plasma cleaning process is performed to oxidize the cracked non-polar R/G/B colorants. Then, a solvent cleaning process is performed by using a non-polar solvent to remove the non-polar R/G/B colorants from the bottom layer.