Earlier quoted context omitted.
It's hard, but people have made progress with that approach: http://recon.cx/en/f/vskype-part1.pdf http://recon.cx/en/f/vskype-part2.pdf
Those links detail reverse engineering the binary. I think Iv's point is that reverse engineering an existing binary is not what "clean room" means.
This was the method used by Compaq to implement the IBM BIOS, back in the day.