The world number one, aiming to add the claycourt crown to Masters titles he won in Indian Wells and Miami this year, was barely stretched as a succession of unforced errors by the 14th seed allowed him to zip through the first set in 22 minutes.
Stepanek steadied himself in the second but never looked likely to make it a contest after he dropped serve in the third game.
"I didn't have to play great tennis on my service game, but I'm pleased with my performance," Swiss Federer said.
"I always try to make as few mistakes as possible and today I managed that, even when I was going for my shots in the first set."
In the last eight Federer will play the winner of the later match between sixth seed Nikolay Davydenko and Spanish qualifier Nicolas Almagro.
