Detach the toilet from the floor, if it is still installed, by shutting off the water supply knob on the wall behind it. Flush the toilet to drain out the water and then unscrew the water line from the back of the tank using a wrench. Unscrew the two floor bolts using the wrench and lift the toilet up from the floor.
Scrape away the wax ring from the flange using a putty knife and discard it. Stuff a rag inside the open floor hole to prevent gas from seeping up into the home.
Install 1/4-inch sheets of plywood on the bathroom floor joists starting at one side of the room. Secure the plywood sheets to the joists using 1-inch-long drywall screws and a power drill, spacing them every 12 inches along the joists. Continue installing the plywood until you reach the area of the toilet.
Sprinkle chalk or powder liberally around the top perimeter of the floor hole. Lay the next sheet of plywood in place as much as possible and press it down gently with your hands. Lift the plywood up to reveal a chalk line around the area that requires cutting.
Trace the chalk line using a pencil in case the chalk begins to rub off. Then lay the plywood on top of two saw horses with the pencil line facing up.
Wear safety glasses and create a hole in the center of the circle using a drill and a 1/2-inch bit. This allows you to insert a jigsaw blade into the plywood. Set the drill aside and insert a jigsaw blade into the hole to cut around the circular line.
Place the plywood into position on the bathroom floor and ensure the hole fits perfectly over the floor hole. Secure the plywood to the floor joists using more deck screws.
Continue installing 1/4-inch plywood over the reminder of the bathroom floor and then install any desired flooring before reinstalling the toilet.