First, you do not NEED to use cement board as a subfloor for ceramic tile. It is the ideal/default material for the job, but it is not necessary, and it often is redundant. As the Lowe's Home Improvement book states, "Many existing floors will work as backing for ceramic tile, including concrete slab and plywood." (p.158)
Cement board is only recommended for its levelness and rigidity so the subfloor does not bend when stepped upon, which will crack the tile. If your plywood is installed on top of a concrete slab, for instance, then you have the required stiffness and can install the tile directly onto the plywood. If the plywood has not concrete underlayment, but is layered to more than 1 1/4 inches, then it is sufficient, as well.
If you are dead-set on removing at least one layer of plywood, then doing so will depend on how the "upper" "sub" floor was attached. If they used nails, then remove them and the floor should pull up. But more than likely (because you otherwise probably would not have asked the question), they used some sort of caulk-adhesive between the layers, which will make the "upper" floor virtually impossible to remove. Even if you get it off, you will likely leave chunks of the old "upper" floor or take up chunks of the "lower" floor. You can sand and fill these spots, but it will be a lot of work.
If the amount of adhesive used makes the job more than you can do in an hour or so, it might be easier to just install an entirely new subfloor. Don't replace more than you need to, but when the cost/time of keeping the old floor exceeds the cost/time of just replacing it all with new floor, just replace it.