The world number one whose French Open title defence starts in just over a fortnight, put in a training session at the Estadio Nacionale, where he is bidding for a second title after 2008.
Federer plays veteran Frenchman Arnaud Clement in Friday's quarter-finals and holds a 6-3 advantage in that series with their last meeting in 2006.
"He beat me twice at the Australian Open, but we've never played on clay," said the Swiss. "His best results have come on hardcourt.
"He's a tough counter-puncher and he makes you do more with your own game in order to beat him. He's not an easy guy to deal with."
While Federer was keeping fit, there was bad news for organisers as ailing French third seed Gael Monfils joined injured number two Croatian Ivan Ljubicic in making a late pullout.
Combined with the withdrawal weeks ago of two-time finalist and 2003 champion Nikolay Davydenko to recover from a broken wrist and the pullout of American James Blake, officials had to be glad that Federer was still in the tournament.
Monfils, ranked 18th but without an ATP start for six weeks due to a hand injury, was unable to play his opening second-round match after being ill throughout the night.
The 2009 French Open quarter-finalist said he spent a rough night and is not sure if he can be ready for next week in Madrid, the last major stop before the French Open which begins on May 23.
"I barely slept an hour last night, I was sick three or four times," Monfils said after pulling out against Spain's Alberto Martin, who later beat compatriot David Marrero 6-1, 6-2.
"After my hand injury, this is more than just bad luck for me. I was so looking forward to playing, to getting back on the court.
"I wanted to use this week as preparation for Roland Garros. Now I don't know when I can play.
"I hope to go to Madrid (from Sunday) but I can't be 100 percent sure. I have to see how I feel. My head is stuffed and I feel poorly."
That setback came a day after Croatian Ljubicic was forced by a tear in a rib muscle to also withdraw.
"The tear was seven centimetres last Thursday, now it only two centimetres," said Ljubicic. "I'm still healing and there is no way I can play.
"I'm pulling out of Madrid as a precaution but I'm optimistic of perhaps playing at Nice the week before Paris.
"I'm sorry I can't play, Now it will be up to Roger to show everyone in the field how to play tennis. I'm confident that if my progress continues, I can start training again next week," said the Masters 1000 champion in March at Indian Wells.
On court in the second round, Spanish fifth seed Guillermo Garcia-Lopez put out one of three Portuguese players remaining as he beat Leonardo Tavares 6-2, 6-2.
Portugal guaranteed itself a player in the final four for the first time here as Rui Machado beat Michal Przysienzy 6-4, 6-4 and Frederico Gil defeated Santiago Giraldo by a similar scoreline.
In the women's WTA draw, second seed Sorana Cirstea of Romania reached the semi-finals over Arantxa Rus of the Netherlands 6-4, 6-1 while Chinese seventh seed Peng Shuai continued her impressive Estoril debut as she upset fourth seed Anabel Medina Garrigues of Spain 4-6, 6-4, 6-3.