Six-time winner Federer and reigning champion Novak Djokovic were home and dry in the quarterfinals, having completed their matches on Centre Court.
The persistent drizzle in southwest London meant only one match was completed on the outside courts in the men's last 16.
Swiss great Federer said Wimbledon officials were right to keep the roof open during his 7-6 (7/1), 6-1, 4-6, 6-3 win over Belgium's Xavier Malisse.
It seemed somewhat of a volte face from the All England Club, having kept the roof closed on Friday as a preventative measure – to the annoyance of some – despite the gloomy skies never breaking.
"I was happy they kept it open because it is an outdoor tournament. We don't want to play indoors all the time. It's not that big of a deal coming on and off," third seed Federer said after his 850th tour win.
"I know spectators would rather see a match than sitting in the rain."
'Drama belongs to Wimbledon'
But, he added: "They love it. To see the referee coming out and inspecting the courts, that's the whole drama that belongs to Wimbledon. Eventually if it's too bad and it's really raining, this is when you shut it."
With the Centre Court roof firmly closed, world number one Djokovic was able to play his match against fellow Serb Viktor Troicki, winning at a canter 6-3, 6-1, 6-3.
And while Federer wants the roof open, Djokovic wants it closed, having got used to it.
"It's all good," he said, grinning.
"It's good for me to finish and to have a day of practice and get ready for next challenge.
"I played only the first match outdoors and then all the three next ones were under the closed roof. It's a bit more humid. The balls get a bit bigger. Maybe the grass gets more slippery on the back of the court.
"They're doing a really good job with arranging the temperature inside. Because when it gets around 15 000 people in the stands, they're really making sure the grass is not too slippery."
Federer knows who he will play in Wednesday's quarterfinals, after Mikhail Youzhny, the 26th seed, triumphed in a tough, five-set battle with Uzbekistan's Denis Istomin.
Youzhny won 6-3, 5-7, 6-4, 6-7 (5/7), 7-5 out on Court 18 to give him another shot at a first win over Federer – at the 14th time of asking.
He was keeping his cards close to his chest on how he planned to go about it.
"It's good for me that I have one more chance against a great player, one of the best players in the world," the Muscovite said after reaching his first Wimbledon quarterfinal on the seventh attempt – an Open Era record for a single Grand Slam.
"I cannot say anything more about that right now because I don't want to talk now how I will play, what happens against Federer.
"I never beat this guy. So just now I can't talk about my dreams, what I have to do on court to beat Roger.
"If he gives you some chances, you have to take them immediately, because maybe you will never have a second chance."
The rain brought play to a stop on all outside courts, meaning the matches were carried over to Tuesday.
British fourth seed Andy Murray was 7-5, 3-1 up against Croatia's Marin Cilic on Court One.
French fifth seed Jo-Wilfried Tsonga was trailing 6-4, 1-1 against US 10th seed Mardy Fish on Court 2.
A lineswoman had to leave the court after being accidentally hit in the eye by a power-packed Fish serve.
Germany's number 31 seed Florian Mayer was 6-3, 2-1 up against French 18th seed Richard Gasquet. The winner faces Djokovic.
German 27th seed Philipp Kohlschreiber was about to get started against US qualifier Brian Baker on Court 12 when the covers went on.
The victor takes on either Tsonga or Fish in the last eight.
Spanish seventh seed David Ferrer and Argentinian ninth seed Juan Martin del Potro will open the action on Centre Court on Tuesday, with the winner to meet either Murray or Cilic.
In women's action, Maria Sharapova was blasted out of Wimbledon on Monday, wilting under a barrage of powerful shot-making by Germany's Sabine Lisicki.
Sharapova, the top seed, lost 6-4, 6-3 to Lisicki, the girl nicknamed 'Doris Becker' because of her big-hitting game, with the blonde German avenging last year's semifinal defeat.
Sharapova will now lose the world top ranking having only retaken it in the aftermath of her maiden French Open triumph last month.
"I certainly had chances. I didn't take them, but I think a lot of the credit goes to my opponent," said 2004 champion Sharapova.
Lisicki will face fellow German Angelique Kerber, who ended Kim Clijsters's Wimbledon career, in Tuesday's quarterfinals.
Four-time champion Serena Williams will face defending champion Petra Kvitova, Polish third seed Agnieszka Radwanska plays Maria Kirilenko while unseeded Austrian Tamira Paszek tackles Victoria Azarenka.
Lisicki (22) had lost in the first round of her last four tournaments, but she hit form at the right time on Monday against Sharapova.
"It's just unbelievable. I had lost the last three meetings with her, so it's nice to finally win one," Lisicki said.
Kerber demolished Clijsters 6-1, 6-1 to reach the quarterfinals for the first time.
Such a humbling defeat was a cruel way for Clijsters to bid her Wimbledon farewell as the four-time Grand Slam winner prepares to retire after the US Open.
"I won't be sorry about anything," Clijsters said. "I know that every time I've played here I've given my best."
Williams dug deep to defeat Yaroslava Shvedova 6-1, 2-6, 7-5.
"I love the drama." Serena said. "I knew the whole time I could play better, but I feel fine. I'm not tired."
Kvitova enjoyed a 4-6, 7-5, 6-1 win over Italian 24th seed Francesca Schiavone.
Unseeded Paszek beat Italy's Roberto Vinci, the 23rd seed, 6-2, 6-2 to book her place in the quarterfinals for the second successive year.
Paszek will play Azarenka, a beaten semi-finalist last year, after the reigning Australian Open champion crushed 14th seed Ana Ivanovic 6-1, 6-0.
Radwanska cruised to a 6-2, 6-3 win over qualifier Camila Giorgi and faces 17th seed Kirilenko, who beat China's Peng Shuai 6-1, 6-7 (8/6). – Sapa-AFP