This is a basic outline for dog urine on or in the wood of your subfloor. Usually this is when the urine has gone through the carpet, pad and into the wood. Wood subfloor is under carpet, tile, vinyl, hardwood etc. The subfloor in the picture is under hardwood. The urine can get to the subfloor through any of these surfaces but in my experience it is usually the carpeted area's that have a problem first. Subfloor is either plywood, particle board, chip board or a similar product. Sometimes you will have carpet tack strip baseboard and even Sheetrock that is contaminated with dog urine. When this is the case you will need to address these items to get complete odor removal.
You need to remove or take up the flooring material (carpet, tile, vinyl, hardwood etc) that is in the area of the damage so you can get to the subfloor to repair it.
If the subfloor is lightly contaminated with dog urine you can give it a light cleaning and a light treatment of odor neutralizer. Take care not to over wet it and cause additional damage. Let it dry and seal it with a good varnish, shellac or an acrylic sealer. Many times it is not possible to completely clean these porous wooden materials. Thus the need to seal them. This will seal in any remaining odor or contaminate.
If the subfloor has started to buckle and warp from the moisture you can use a skill saw. Set the blade to the depth of the thickness of the floor (3/4 inch usually) and cut an x through the middle of the warped area. The thickness of the blade will remove enough wood material so you can then fasten the subfloor wood back down flat to the floor and support beams underneath. Use flooring screws for this. You may need to make two cuts depending on how warped the wood is. You just need to remove enough wood so the subfloor will lay flat again.
If the wood is too damaged and warped to repair it this way, then again set the blade to the thickness of the wood and cut the damaged area completely out. Cut a new piece of subfloor material to fit, and replace the bad piece. If there is any urine residue left in it anywhere clean and seal that area with the before mentioned sealing products. Then you will need to replace the section of pad and reinstall or replace the carpet. If you reinstall the carpet you will obviously need to clean and treat it (front and back) first.
Or replace whatever flooring material the damage is under. (Tile hardwood vinyl etc.) If you have questions post them below and I will respond.