Federer will play in the second round of Dubai on Wednesday against Fernando Verdasco.
The Swiss has been on 99 career titles since last October when he won in Basel.
On Monday, his half of the draw in Dubai saw Milos Raonic exit the tournament to Jan-Lennard Struff.
Then big-hitting Russian Karen Khachanov lost in straight sets to Nikoloz Basilashvili.
And today, potential final opponent and third seed Cilic was beaten by in-form Frenchman Monfils.
Monfils, who won the Rotterdam Open earlier this month, came through 6-3 4-6 6-0 to seal his place in the second round and will play Marcos Baghdatis on Wednesday.
Defeat is a blow to Cilic, who speaking prior to the event spoke about his desire to make an impression on the Grand Slams this year.
“It doesn’t bring any extra pressure or weight. For me it’s a motivation, I feel that I’m close, my game is good enough to win grand slams,” Cilic said.
“Also my desire is bigger to train and do the right things.
“I’m feeling I’m improving, I’m getting better, so that at the end of the day is the most important thing for me, the satisfaction that gives me out of my tennis and I can get myself back on the court and enjoying tennis.
“I’m loving that and who knows what can happen until the end of my career?
“I would be anyway satisfied if I finished it today, it would be sad but still I would know that I did all I can.
“But still I think there are many more things that I can do to try to see how far I can go.”