"It's been a really difficult week for me, so I'm happy to have played a decent tournament," said Federer, the defending champion in the year's first ATP Masters tournament, who struggled throughout with an aching back.
"Overall, under the circumstances, I'm happy," he said, adding that he expected to stick to his planned schedule of taking a lengthy break, up until the Madrid Masters in early May.
Last year, Federer, who went down 6-4, 6-2 to old rival Nadal, arrived at Indian Wells with victories in Rotterdam and Dubai under his belt.
The 31-year-old was denied title repeats in both of those events — losing in the semi-finals in Dubai after failing to convert three match points against Czech Tomas Berdych.
A return in Madrid would see him again trying to defend one of his six 2012 titles, which also included a Wimbledon crown and a win in Cincinnati.
"I'll probably maintain my schedule, but you never know," said Federer, who was heading back to Switzerland.
"I always say I will discuss with my team what the schedule is after here once the tournament is over."