I'm going to buy a fixer,and when we went to see it the renters had 2 dogs and 3 cat NOT ONE of them was house broke. Guess how it smells!! Can we clean the carpets and floors or will we have to pull them up? If we pull them up do we have to pull the sub-floor and replace it or can we paint the sub-floor?

I think you will be better off taking up the carpet and pad. There is a product called Odor-Ban which you can use of the sub-floor. Let it dry well and if needed, you can "seal" the sub--floor before laying new pad and carpet. I don't think you will ever get the smell out of the existing carpet. And all that has soaked into the padding(which is foam, like a sponge). I just remodeled a house where the previous owners had dogs and you would not believe the difference when the carpet was taken out!
Good Luck--