Federer eased past 30th-seeded Italian Andreas Seppi 6-3, 6-4 at the first ATP Masters 1000 event of the year. The Swiss native has won this event four times and was last year's runner-up to Novak Djokovic.
Third-seeded Nadal, who has titled here three times and was a runner-up to Djokovic in 2011, overcame early adversity and cruised to a 6-4, 6-2 result over Donald Young at the Indian Wells Tennis Garden.
Next up for Berdych will be 27th-seeded fellow Czech Lukas Rosol, who outlasted Dutchman Robin Haase 6-4, 6-7 (4-7), 7-6 (7-3) on Day 6.
In other action, 17th-seeded Spaniard Tommy Robredo defeated 11th-seeded Gregor Dimitrov 6-4, 1-6, 7-5 in a match that lasted just under two hours and Jack Sock dropped 15th seed Roberto Bautista Agut 3-6, 6-3, 6-2 win.
This week's champion will collect $900,400.