After pulling up old carpet in my house, the subfloor was stained everwhere. what's worse is that the dampness left a horrible odor. I am not sure if you are putting down new carpet or trying to save the floor, but here's what I did. I bought some "Nature's Miracle" from a pet store and sprayed down all the stains. The enzymes eat away at the uring crystals which cause the smell. After it dried, I primed the floor with Zinnser's BIN to seal the floor. From what I hear, this BIN is used on smoke damaged walls in houses that had fires to seal in the smokey smell. we have not layed the carpet yet, but the smell is all gone. Sealing the floor is key.