The endonuclease activity of FENs was initially identified as acting on a DNA duplex which has a single-stranded 5' overhang on one of the strands (termed a "5' flap", hence the name flap endonuclease).
Some FENs can also act as 5'-3' exonucleases on the 5' terminus of the flap strand and on 'nicked' DNA substrates.