DNA endonuclease activity, producing 3'-phosphomonoesters flap endonuclease activity 3'-flap endonuclease activity Catalysis of the cleavage of a 3' flap structure in DNA, but not other DNA structures; processes the 3' ends of Okazaki fragments in lagging strand DNA synthesis. molecular_function GO:0048257 3' flap endonuclease activity