The cast Iron flanges that I install with lead and oakum slip over cast iron pipe.Iif this is the case with yours then I would remove the existing flange with a hammer by breaking the flange portion off and using a cold chisel to split the flange in two places. The flange would then fall off the pipe.
I would then cut the pipe off witha grinder at my finished floor height. after the finished floor is installed I would lead in a new cast iron flange.
Goodluck to you.