If you have a cat, the small Compact Deep Cleaner may help. Here

http://www.amazon.com/BISSELL-Little-Multi-Purpose-Compact-Cleaner/dp/B0016HF5GK

Follow the instructions of the cleaner and you will solve the problem. I found this helpful. BTW, have you prepared a litter box for the cat? I think he's just got scared and nervous. Give him some time. He will adjust himself. If you couldn't handle the cat, return him to the shelter. Don't just drive him out.