Federer, who has now won 21 matches straight and is going for his 11th title of the season after winning the Madrid Masters last week, was flawless as he continued his path to the final of an event that he has never won, but dearly wants to.
"I can't believe how well I'm playing," said Federer who has lost two finals and was also a ballboy at the Basel tournament.
"The match went so quickly, I just did everything well."
The 25-year-old is aiming to win his fourth tournament in a row after victories in the US Open, Tokyo and Madrid, helping him to an 84-5 win-loss record this season.
Meanwhile, Federer's Swiss Davis Cup teammate Stanislas Wawrinka eliminated two-time champion Tim Henman with the Briton hampered by a pain from a longstanding right knee injury.
Henman, after sailing through the first set, began to struggle with his ailment and went down 2-6, 7-6, 6-4 in a second-round loss.
"I'll have a scan tomorrow and we'll see," said Henman.
"I'm not 100 percent sure what it is. In the second set I felt a few sharp pains, especially in longer sprints along the baseline."
Defending Basel champion Fernando Gonzalez survived six match points as he held on over American Mardy Fish 6-7 (5/7), 6-4, 7-6 (10/8).
Third seed Gonzalez is has had a tough few months after an exhausting European indoor campaign.
"Every week is different, with the court, the balls, everything," said Gonzalez, who is ninth in the chase for one of the four remaining spots at next month's season-ending Masters Cup in Shanghai.
"I have no choice but to play well here and in Paris," he added.
In other results, Thai Paradorn Srichaphan defeated Argentine Juan Chela 6-4, 6-3 and will meet Chela's compatriot Jose Acasuso who defeated German Philipp Kohlschreiber 7-6 (7/1), 6-1 in the next round.
Fifth seed David Ferrer ousted former champion Jiri Novak 2-6, 6-3, 6-3 while second seed David Nalbandian survived a scare as he won a draining match over Spain's Feliciano Lopez 6-7 (4/7), 6-3, 7-6 (9/7).