The inside pipe cutter will only work if you have enough pipe from the hub of the flange to the hub of the 90. You should find out first what kind of flange it is, it could be one that either slips into 4" pipe or over 3" pipe, if it slips into a 4" drain then cutting top of flange of and notching the fitting without going through the actual drain pipe, like what was mentioned before, or if it is slipping over 3" pipe and you do have enough pipe to add a new fitting the the inside pipe shooter(cutter) will work.

And if its a off-set flange, then its a whole new set of problems.