Rafael Nadal, Robin Soderling, Novak Djokovic and Nikolay Davydenko kick off Group B on Monday.
In Thursday's quarterfinals, fifth seed Robin Soderling of Sweden takes on No. 13 Mikhail Youzhny of Russia.
Del Potro looked weary after his epic three-set semifinal win over Swede Robin Soderling the previous night.
Sweden's Robin Soderling progressed in straight sets as he overcame the serve of Janko Tipsarevic 6-3 7-6 (7-5).
Nadal's only loss at the French Open came against a similar player in 2009, the two-time finalist Robin Soderling.
Elsewhere, fifth seed Robin Soderling of Sweden beat Italian wild card Paolo Lorenzi 6-1 7-5 to reach the third round.
In Wednesday's quarter-finals, Federer will face Sweden's Robin Soderling, the fifth seed, while third seed Novak Djokovic takes on Frenchman Gael Monfils.
Eighth seed Robin Soderling remains the only player inside the top 12 to have been eliminated after he lost in the opening round.
However, world No. 8 Robin Soderling was knocked out in the first round of the Chennai Open in India, where he was top seed.
CNN: Federer and Nadal cruise as nemesis Soderling crashes out
However, 16th seed Berdych never approached the form that saw him stun the world number one, as well as French Open finalist Robin Soderling.
Sweden's Robin Soderling, a French Open finalist, dropped the first set of his opening match before eventually seeing off Tommy Robredo of Spain 4-6 6-1 6-4.
In the other matches Italy's Davide Sanguinetti overcame France's Gregory Carraz 6-3 2-6 7-5, while Robin Soderling of Sweden beat Juan Ignacio Chela, Argentina 6-4 6-3.
The 28-year-old Davydenko, who won the Paris title in 2006, will next play either big-serving Croatian Ivo Karlovic or fellow London hopeful, ninth-seeded Swede Robin Soderling.
Third seed Robin Soderling beat Nicolas Almagro 7-5 4-6 6-3 to set up a clash with eighth seed David Ferrer, who beat Lu Yen-hsun 6-3 3-6 6-1.
Last year, Federer struggled past Sweden's Robin Soderling in his first match, losing the first set, but went on to beat Russia's Marat Safin in the final.
Murray next plays Roland Garros finalist Robin Soderling, who reached the quarterfinals in California for the first time after beating ninth seed Jo-Wilfried Tsonga of France 6-3 6-4.
Swedish ninth seed Robin Soderling kept alive his hopes of snatching a place at the ATP World Tour Finals in London by defeating Croatia's Ivo Karlovic 6-4 7-6.
O'Shannessy gave an example of a more typical Nadal match: the 2010 French final against Robin Soderling, the only man to beat Nadal in Paris (that was in 2009).
WSJ: Rafael Nadal, the Underrated Tactician, Stalks Novak Djokovic
But Federer was, if anything, even more impressive as he destroyed Robin Soderling 6-1 6-1 to set up the chance of revenge for that defeat by Djokovic at Flushing Meadows.
Berdych continued his giantkilling run as he followed up his victories over world No. 1 Roger Federer and 10th seed Fernando Verdasco by crushing Swedish fifth seed Robin Soderling 6-2 6-2.
CNN: Roddick serves up semifinal upset with victory over Nadal
Roddick defeated Swedish sixth seed Robin Soderling 6-4 3-6 6-3 in a showdown between two big servers in the later semifinal to earn his first shot at the Indian Wells title.
Seventh seed Jo-Wilfried Tsonga beat Colombian qualifier Santiago Giraldo 6-3 6-4 and will face Ferrer in the last eight, while fifth seed Robin Soderling went down 6-3 6-2 to Stanislas Wawrinka .
That appeared to deflate Murray and the 23-year-old Scot was broken again as Ljubicic moved through to a semi-final encounter with eighth seed Ferrer, who upset Sweden's third seed Robin Soderling 6-2 6-4.
Defending champion Federer meets Australia's Peter Luczak in the first round, but could face his fellow Swiss Stanislas Wawrinka, last-year's runner-up Robin Soderling, Latvia's in-form Ernests Gulbis and Murray en route to the final.
World number one Rafael Nadal will face Florent Serra in the second round after the Frenchman beat Guillermo Canas, and there were first-round wins for Radek Stepanek, Ivan Ljubicic, Philipp Kohlschreiber, Robin Soderling and Andy Roddick.
Davydenko, who beat Rafael Nadal, Robin Soderling and Roger Federer on his way to the final, was sharper throughout as Del Potro appeared to be feeling the after-effects of his semi-final win over Soderling the previous evening.
Berdych, the 16th seed, beat Argentine Horacio Zeballos 6-4 7-5 to secure his place in the next round, while fifth seed Robin Soderling of Sweden was more impressive in a 6-1 6-2 hammering of Germany's Philipp Petzschner.
Fifth seed Robin Soderling of Sweden progressed with a 6-0 6-7 (3-7) 6-2 victory over Chile's Fernando Gonzalez, while Mardy Fish of the U.S. was forced to retire while trailing 6-1 1-0 against 13th seed Mikhail Youzhny.
World number two Nadal has not played since losing in the fourth round of the French Open to Robin Soderling, troubled by tendinitis in both knees which caused him to skip his defense of the Wimbledon title.
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