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Against Djokovic, Federer will be working for his 16th career Masters 1000 trophy, which would put him one short of the all-time record of Andre Agassi. Federer owns three titles this season -Madrid, Paris and Wimbledon.
Federer, a two-time Cincinnati champion, earned the win without facing a single break point.
The victory was only the third for Federer against the 22-year-old Murray, winner along with Nadal of five titles this season, including the French Open and Wimbledon.
Federer improved to 46-7 on the season while Murray suffered his eighth loss of 2009 and will head to New York as soon as possible to prepare for the Open starting August 31.
Murray said he's more than ready to head to the Grand Slam after winning the Montreal title last week and getting to the final four in Cincinnati.
'I played seven, I thought, very solid matches,' said the Scot, who added: 'Yesterday and today weren't so good. That could have (come) down to a combination of things: My opponent was playing well, my level dropping slightly.
'But it's been perfect preparation for the US Open. I'll go there this evening or tomorrow and rest up for a couple days and train hard before it starts.'