Federer will play James Blake, who edged Philipp Kohlschreiber 6-4, 6-4, and the fourth-seeded Murray will face defending champion David Nalbandian.
Nalbandian defeated Juan Martin del Potro 6-4, 6-0, and Andy Roddick overcame Gilles Simon 6-3, 7-5 to seal his spot in the Masters Cup.
Federer used an ace to finish the dominant win over the 20-year-old Croatian, while Murray clinched his 14th straight win and improved to 5-0 against his Spanish opponent.
Murray looks to become the only player to win three straight Masters titles after victories at Cincinnati and Madrid.
Federer could reach the semifinals at the Paris Masters for the first time. He reached the quarters in 2002 and 2003.
"I had better results in other tournaments, that's for sure,'' Federer said. "Of course, I prefer to come back to a place where I had success in the past. This is not the case here.''
Federer is 8-1 against Blake, with the Swiss star's only loss coming in the quarterfinals at the Beijing Olympics in August.
"I'm not the revengeful type, but I would be pleased to beat him,'' Federer said.
Roddick needed five match points to get the better of Simon. The American will play No. 13 Jo-Wilfried Tsonga, who beat No. 3 Novak Djokovic 6-4, 1-6, 6-3 in a rematch of the Australian Open final.
"If I manage to stay in shape physically, I will go from strength to strength in this tournament,'' Tsonga said.
The Masters Cup in Shanghai features the top eight players in the ATP race. Blake remains in contention, and Simon can qualify for the tournament if other results go his way.
Roddick felt he had to dictate the pace against Simon.
"It wasn't going to do me any good to play patty-cake back and forth with him,'' Roddick said. "I'm not as quick as he is and I'm not as consistent as he is. It actually made for a pretty simple game plan. "
Later, top-ranked Rafael Nadal meets No. 16 Gael Monfils.
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