A novel two-step acetone treatment method was developed to enhance the enantioselectivity of Candida rugosa lipase (CRL) toward the hydrolysis of racemic naproxen methyl ester. The acetone-teated CRL was considerably more enantioselective than the crude CRL, yielding an enantiomeric excess of 98~100%. The crude and acetone-treated CRLs were subjected to anion exchange chromatography, and their chromatography profiles were compared. In consequence, both chromatography profiles were found to be almost identical, resulting in two separate lipase peaks (lipase A and B). The lipase B, which is known to be less enantioselective, was treated with acetone using a two-step treatment method. The enantioselectivity of acetone-treated lipase B was dramatically increased, yielding an enantiomeric excess of 99%.