If the flange actually is too high, the replacement method depends on the type of pipe you have. If you have cast iron, you need a plumber to remove the old and do the replacement as this is done with molten lead, not a DIY job. If it is ABS or PVC, it still would be wise to get a plumber because the old flange must be cut out with tools you and I don't have. As already noted, the flange is supposed to set on top of the finished floor and be screwed into the sub floor.