Absorbent cleaning rags will help sop up the mess. When not cleaned up immediately, pet urine stains and odors can seep below your flooring surface and into the subfloor. Removing urine from subfloors takes elbow grease, but the reward is a better-smelling, more sanitary home and a well-behaved pet.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.