After removing carpet to sub floor should I treat the subfloor wood?

The subfloor needs nothing except a good vacuum. If it's hardwood, then you can look into oxalic acid to bleach stains.

I wouldn't use bleach, I'd try a wood cleaner that's stronger than Murphy's oil soap. You want to clean and disinfect before you lay new carpet down. Make sure the floor is completely dry. Also, check for loose boards, they made need a nail or two, otherwise the floor will squeek in the winter, and squeek in the summer because the boards are expanding from the heat. EJL

http://www.howtocleanstuff.net/how-to-clean-particle-board-subflooring/

After cleaning paint with an oil based paint before you put your next flooring down. I had to do this in a rental to get rid of the cat pee and smell. I had spent 5 days soaking and mopping the area with a mixture of hydrogen peroxide and baking soda, can't remember the recipe but got it online. It was a gross job but worked thankfully. the oil paint seals in anything you are not able to remove. Good luck

Just be sure to remove staples, and pour floor leveling compound if you are doing hard flooring or vinyl.

Are there hardwood floors underneath or just your typical plywood?

It's a builders grade plywood floor and I will be putting down hardwood flooring. Thanks for all the help. The stains are not cat pee? Where do I buy leveling compound?