I have a live in male dog that has been marking his territory in the home. I want to replace carpet with hardwood, but am afraid of what urine woukd do to the hardwood flooring. Does anyone know if there a polyurithane that would seal the wood and prevent any urine from absorbing into the flooring?? Also, is it possible to put in pre-finished flooring and then a coat of polyurithane over the flooring as well?

No, your asking for the impossible with the chemistry available today.

No matter what you do, it will damage the flooring and the finish. It is like paint stripper...almost.

So the amonia in the urine is strong enough to strip the finish? Wow...

Most pre-finsihed floors gain nothing from having an additional coat of finish put on after they are installed. This is something you could do down the road as a maintenance program, but un-necessary for a new installation.
And yes, if the dawg is a "live-in" type animal, you will have to accept his wild heritage, or have him fixed. (broken?)
If you are talking about just going to bathroom rather than marking his territory, try to train him to use an area dedicated to him for that purpose. Not easy, but can be done.

I think I should just wait til the dog leaves then to put down any flooring....Thank-you very much for taking the time to help me out.

Austin knows, he has two that live indoors. But I am sure he has then trained. Or at least I hope so.

Trained or not, Otto is a disaster waiting to happen!! He is not a year old yet and he weighs over 100#(both his parents are under 65#)

Otto needs to get a job .