I think you can still use them. You would probably prep the rough opening the same way as you would a new construction window, with a sloped sill (using cedar siding) and flashing installed in the correct orientation and locations. The important part will be how to you water proof it without a flange, but that will depend on how the window is constructed. If you wanted to get fancy you could probably even make a flange from aluminum stock and a good caulk like OSI quad max or something.