Others seeds to progress were Mikhail Youzhny (20) and Nicolas Almagro (26) and Albert Montanes (31).
Fourth-seeded Spaniard Montanes moved into the last four by beating Uruguayan eight seed Pablo Cuevas 6-4 6-3.
Murray faces Spain's Albert Montanes in the second round after his opponent Andrey Golubev retired at 6-2 3-0 down.
Defending champion Albert Montanes moved into the last eight with a 6-1 6-2 victory against fellow Spaniard Daniel Gimeno-Traver.
Murray has now played Montanes four times and is yet to concede a set against the world number 24.
Montanes won the first two games of the second set before Murray reeled off five straight games to put himself firmly in control.
However, the errors crept in for Montanes and a forehand winner from Murray at break point proved decisive and got the match back on serve.
Ninth seed J uan Martin del Potro was also taken to four sets before the Argentine beat Spanish veteran Albert Montanes 6-2 6-7 6-2 6-1.
Del Potro had beaten Montanes for the Estoril title in April.
That pair were joined in the quarterfinals by three other Spaniards, with Albert Montanes producing the shock of the day by dumping out fourth seed Marin Cilic 6-4 6-4.
"Maybe I did, but I don't remember, " said the Swede, who will play Albert Montanes in round three after the 29th seed waltzed past Tobias Kamke 6-3 6-2 6-1.
Ferrer, who plays fellow Spaniard Albert Montanes next, will be hoping that his shoulder improves significantly over the next few days: he has lost three finals and counting to Nadal.
The first four games went with serve - Murray winning both of his to love - but the Scot was stunned in game five when Montanes capitalised on his fourth break point with a stunning cross-court backhand winner.
Federer is on track to win back the title he claimed on his only other appearance at Estoril in 2008, but admitted he was not yet at his best ahead of Saturday's semifinal clash with defending champion Albert Montanes.
Djokovic is likely to be waiting in the semis as he next takes on Italian Fabio Fognini, who won an incredible five-set match against Albert Montanes over more than four hours, despite being barely able to move by the end.
Top seed Djokovic, who lost to Nadal in last year's final, was in impressive form as he cruised past Argentine David Nalbandian 6-2 6-3 -- and he will now face either sixth seed Fernando Verdasco or Albert Montanes in the semifinals.
Home hopes were boosted by an easy straight sets win for seventh seed Andy Roddick over Thiemo de Bakker of the Netherlands while in-form Jo-Wilfried Tsonga of France was taken to three sets before beating Albert Montanes of Spain, 4-6 6-3 6-3.
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