After reading different post I'm not clear what to secure a new toilet flange to. I had to replace the subfloor and I am getting ready to put down 1/2 inch cement board and then new tile. Would you recommend placing the flange on the cement board or on top of the tile or on the subfloor? I can still cut the pvc leading to it to any length.
Thanks for your help!

Your flange should sit with its bottom surface at the tile surface. Screw your flange into the sub floor after glueing. You can also use a PVC Oatey Twist-N-Set flange that sit inside your 4 or 3" drain, no glueing and it is removeable. It has three screws that cause a neopreme band to expand and seal.

Thanks for the quick response. So do I screw through the tile and cement board or don't have them under the flange just having the flange raised to the height of the tile? Thanks again... this is all new to me

You should get your cement board right up to and around your drain, same with the tiles. The tile can have some gaps so you can get your screw into the subfloor without drilling into the tile. Male sure your modifed thinset has cured for several days before setting the toilet.