Mandi has it but you may also need to get a oversized wax ring along with longer bolts. Once you remove the toilet, clean out all the wax and you will find that the bolts installed use a slotted design so you can slide them and remove them. Go to the local hardware/home project store and tell them what you are doing and they should take you to the plumbing section and set you up with longer screws and the larger wax ring so that once you install the tile around the drain (so that it goes under where the toilet will sit) you can install the screws, then the wax ring and then the toilet.
Best of luck!
Best of luck!