Step 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.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.