The World No.2 had suffered from a back injury in his last outing at Indian Wells at the beginning of March, but he looked comfortable on his first appearance on the clay in 2013 against the World No.48.
The 17-time Grand Slam winner got off to the perfect start as he broke in the third game before holding serve to take the first set 6-3.
And Federer broke Stepanek again early in the second set to move ahead 3-1 before breaking once more to serve for the match at 5-2.
However, he was then broken himself for the first time in the match as Stepanek finally took a break point opportunity at the eighth time of asking.
That only delayed the inevitable though as Federer broke again in the very next game to seal the win.
Next up the three-time champion in Madrid will face either 14th seed Kei Nishikori or Victor Troicki on Thursday.
Madrid Open: Roger Federer cruises past Radek Stepanek
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