Top-ranked Novak Djokovic pulled out ahead of his quarterfinal against 2008 champion Jo-Wilfried Tsonga of France, saying a nagging shoulder injury got worse after his third-round comeback win against fellow Serb Viktor Troicki on Thursday.
Federer hit seven aces and 25 winners -- compared to only eight for Monaco -- to become the seventh player to reach the 800-win plateau. He joins Jimmy Connors (1,242), Ivan Lendl (1,071), Guillermo Vilas (923), John McEnroe (875), Andre Agassi (870) and Stefan Edberg (806).
"I knew going in today that this could be something special, something I could remember," the third-seeded Swiss said. "So it's just another win, but it's a special one nevertheless, because 800 is definitely a big number."
Federer won five straight games to rally from a 3-1 deficit and took the first set when Monaco netted a backhand. The 16-time Grand Slam champion broke for a 6-5 lead in the second when Monaco made a forehand error, winning the match with an ace.
Earlier, Berdych saved 15 break points to end Murray's 17-match winning streak.
"It was really one of the best of three-set matches I played," Berdych said. "It was so close ... it could go the other way. We could be finished after two sets maybe."
Murray broke Berdych in the seventh game and took the first set with a crosscourt forehand winner. The second-seeded Briton rallied from a 5-2 deficit in the second to force a tiebreaker, but Berdych hit a forehand winner to even the match at a set apiece.
In the final set, Berdych broke for a 5-4 lead when Murray double-faulted and held serve to clinch the victory.
"You obviously have to do a lot of running at times. He kind of dictates what happens," Murray said. "At the end, I was just fighting."
In the late match, Isner hit 34 winners to 26 for Ferrer to reach the semifinals of a Masters tournament for the first time. He is the only unseeded player left in the draw.
"I'm just thrilled to have won tonight, given that Ferrer is such a tough player," he said.
Isner took a 4-1 lead in the first set, which he clinched with an ace, but sent a forehand wide at 3-2 to drop serve in the second. The fourth-seeded Ferrer leveled the match when Isner netted a forehand return.
In the final set, Ferrer sent a forehand long to let Isner break for a 5-3 lead, and the big-serving American sealed the win with an ace.