I had a toilet flood and when I removed the flooring (carpet) the floor was rotten. I have removed the plywood. I need to replace the plywood and we now want to install tile. Do I cut out the old flange and raise it to the level of the tile or should the flange be below the tile?

Tile should run under toilet flange. Top of flange can be flush with top of tile. What kind of pipe, cast iron, ABS or PVC. You can pruchase extensions for flange.