Step 1. Remove the carpet or floorboards to access the subfloor. Train a black light on the floor to find spots where there is urine staining. Reapply enzymatic cleaner directly to the subfloor and let sit until it completely dries.Enzymatic cleaner works on any porous surface, including concrete and wood.tep 2. Sand the subfloor down if the stain or smell is very stubborn. Gently remove the surface stain with a sander, being careful not to sand too deeply. You do not want to sand enough to change the height of the floor.