The present invention is directed to methods and apparatus for cutting filaments percutaneously. The methods and systems may be used in conjunction with sealing a puncture percutaneously in tissue separating two internal portions of the body of a living being with an anchor, a sealing plug and a filament connecting the anchor and sealing plug. The present invention provides for safe filament cutting below the skin and may reduce the risk of cutting the filament distal of any knots.