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The fourth seed took just 52 minutes to see off his veteran opponent from the Czech Republic.
Federer, who has been runner-up at the tournament three times, shot out to a 5-0 lead in the first set before Stepanek held to love in the sixth game to finally get on the board.
The set was over in the next game as Federer took his first set point at 40-15.
In the second Stepanek was broken straight away but then had his best period of the match, staying in touch before failing to convert on two break points to level the set in the sixth game.
Federer punished him by breaking in the next and then served out the match.
Next up for the Swiss in round three is another Czech in Lukas Rosol.