The first (well-known) 'clean-room' implementation was when Phoenix implemented an IBM PC-compatible BIOS by having one team studying the IBM source (which was available), then writing up a specification for how it worked, handing that specification over to somebody else (they were Phoenix' legal team, IIRC), which then handed the specs over to another team that had never seen the IBM source. They sat down in their "clean room" (b/c it wasn't tainted by actual IBM source) and implemented a BIOS from specs only. In that way Phoenix was protected from any claims of copyright infringement: Nothing was copied, and the people writing the code had never seen the original source.
In that particular case the specs were reverse-engineered from actual source, but that's not a necessary part of the process. It's more common to have one team study the protocol, data going over the wire, disassembling, etc, then use the knowledge gained to write specs, and then another team implements the equivalent functionality from specifications only.
