I am remodeling my bathroom and removed the old marble tiles which were resting on a bed of mortar on top of 3/4 in plywood. I have chipped away most of the mortar and Im down to the plywood which isn't to smooth. Is it safe for me to install the ceramic tiles on top of this rough plywood? Thanks Liz"

No, you can't install ceramic on plywood like this. The old bed was there for a reason. You need to install a new base like Hardiebacler, Wonderboard , cement board, etc... Screwedand glued to the ply. Your toilet flange will not match the new floor unless you move the flange or build the new floor up to the old height