Cliff Lee did NOT clear waivers
All this means is that a team, or possibly more than one team, filed a waiver claim on Lee. It is, presumably, possible that the Phillies would just say "Bye-bye!" and let the claiming team have Lee and the (approximately) $92 million and three years (plus a fourth-year buyout) left on his contract.
That doesn't seem logical after the Phillies just spent $140 million-plus to retain Cole Hamels; it would seem to indicate that the Phils want to keep their core together. On the other hand, maybe that sort of salary dump would help pay for the Hamels contract.
Complicating matters for any claiming team is the fact that Lee can block a deal to 21 of the other 29 clubs.
The Phillies now have 48 hours to either: withdraw the waivers, in which case Lee can't be waived or traded for the rest of the year; work out a deal with the claiming team, or award the contract to that team, as noted above. As always, we await developments.