I have this hamster cage: http://www.petsmart.com/product/index.js…
And I love it compared to the plastic ones, but my hamster always stays at the top in the wooden house a pees on the wood. How can I clean it and get the smell and stains out. And is there anything I could do to the wood so its protected, but that is safe for pets??? Thank-you!!

Wood should not be used for bases, etc. of hamster cages. They are mainly used for chewing and teething. Because, as you said, are very difficult to clean.

My only solution I can think of is a litter box. You can train your hamster to use it. I'm sure there a lot of videos on youtube about it.

Try getting a litter box. You can't clean the wood and most of the products available to protect wood are highly toxic to rodents. I would suggest to throw out the wood because if your hamster continues to pee on it ammonia will build up. The fumes from the ammonia are toxic and can kill your hamster.

hamster owner