If the flange is secure, you actually can leave the flange "as is" with the layers right under the flange ring. I write that because if you damage the flange it can create a whole new can of worms if the flange or flange-to-pipe connection was damaged and had to be repaired/replaced. However, I'd cut the plywood back closer to the flange, I'd cut back at least to the same size as the first layer that's on top of the plywood in the photo. You might find that the closer to the flange you cut, you can then dig out the layers under the flange. If you get there, then you can simply install new layers of your flooring sandwich around the flange. The new layers don't have to go under the flange, the new layers can encircle the flange. However, if yo have, say, a 3/4" gap between the top of the subfloor and the bottom of the flange, then just cut some small wood blocks (say four blocks, 1" square and 3/4" high for example or sized as needed) that will fit snugly between the flange and the subfloor, and set the blocks around the flange at the 3, 6, 9, and 12 o'clock positions. Keep the blocks clear of the flange bolt locations. The flange itself should be securely attached to the waste pipe beneath. Use a putty knife or equivalent to scrape away the residual wax. Toilets are pretty easy to install, but if this is your first time I do have a recommendation. Use a waxless adapter. Something like the Fernco. Size the waxless adapter to the size of your waste pipe. The thing is that wax rings are "one and done" things. If you set the wax ring, then set the toilet, but then you have to pull the toilet up again to reset it, technically you would want to scrap away the deformed ring and install a new ring, even though the ring you just installed is only 10 seconds old. Once a wax ring is deformed you can't really count on it to give you a good seal the second time the toilet is set. With the Fernco, you set it on the base of the toilet. Then you can set the toilet, pull it, reset, pull, reset, etc. It's good forever, so to speak. You can set a toilet that is fully assembled. Again if you think the weight might be a problem, you can remove the tank from the bowl. then just position and set the bowl. Then reinstall the tank on the bowl. Then shim the base, snug the bolts, and there you go. And as always, do NOT overtighten any of the bolts that go through the china. Snug them up but don't crank down so hard that you overtighten them. You don't want to crack the china. If the base wobbles on your new floor, don't try to make it wobble-free by cinching down hard on the flange bolts. Use toilet shims between the tile and the toilet base. Then snug up the flange bolts. Buy a new set of flange bolts too. Good luck and happy toileting!

That's true, I didn't consider that it might be cast iron. If's its in a basement, and the floor is easily replaced, it may be worthwhile to take up the flooring, open the slab and dig a little. Messy, labor intensive operation though. I guess the solution will depend on the location of the affected appliance and the tools/skill level of the homeowner. I think lazypups idea of using the sheeted PVC to make a shim in the shape of the bottom of the bowl is probably the simplest solution. You could probably easily fashion one yourself (plywood?) if you can't find the material locally.

Its a compression fitting that's easily removed with a wrench and a pipe or fitting extension added. A previous owner of my house replaced a toilet valve and it failed and flood the bathroom so you might want to call a plumber. You also might be able to cut the paneling around it and install a larger escutcheon or omit it. There is usually enough space behind a toilet for paneling and cellular PVC T&G paneling is usually 1/2" thick. A base board the same height as the pipe might allow a tight fit with no escutcheon or extension. Horizontal paneling would be easier to install and I think its more attractive. If you do vertical paneling you will need something behind the drywall to nail it to. You definitely need to replace that crappy shut-off valve. You should only need to turn it a quarter turn to operate it.

Most of these are made with a flange for the toilet and a short downpipe that fits into or over the drain pipe in the floor. It appears that you had an ABS (black) pipe, and there is a PVC closet flange (white pipe on the inside) cemented into it. Then someone cut off the PVC pipe right at the floor level. To get the white pipe out you should be able to use a chisel to cut the ring at one point (chisel straight down), and then drive a flat screwdriver between the white and black pipes. It should just gradually peel away as you work your way around. However, it won't leave the black pipe smooth inside, so you will have to sand it before installing a new flange. Some new closet flanges are designed for 3" pipe and some for 4" pipe, and some are designed to fit either size. You might want to look for a flange made of ABS plastic to match your drain, or if its PVC make sure you get the right cement for PVC to ABS. Bruce