Discovery astronaut Steve Robinson described it as "a ride of a century" as he was maneuvered through space to the shuttle's belly and gently plucked filler material sticking out from tiles in two places.
"My eyes have never seen such a sight," Robinson said.
NASA responded to the successful mission: "Nicely done, Steve."
Robinson's wireless mounted camera provided a spectacular view of the shuttle's underside.
"Stand tall and lean forward," NASA's mission control told Robinson as they moved him closer for the repair.
Robinson was positioned within inches of the haul and reached his gloved hand out to delicately remove the protruding material, reports CNN.
The so-called gap-filler cloth protects the craft's heat-shield tiles from damage as they expand in higher temperatures during takeoff. Mission managers said they are afraid the strips of cloth, which are 0.6 inches and 1.1 inches long, may have caused overheating as the ship reenters Earth's atmosphere.
"That came out very easily," Robinson said after pulling out the second piece of fabric. "It looks like this patient is cured."
Robinson and fellow astronaut Soichi Noguchi opened the hatch of a station airlock at about 4:48 a.m. New York time to begin the spacewalk, the National Aeronautics and Space Administration said. The pair first installed an external platform on the station to be used to store spare parts and tools for future spacewalks, NASA said.
According to The New York Times, at 10:21 a.m. Eastern time on Tuesday, the astronauts received a call from the White House. Seen via video link, they bobbed gently as they waited for President Bush to get on the line, their hair puffing up without the restraining force of gravity. Speaking from the Roosevelt Room, Mr. Bush said: "I just wanted to tell you how proud the American people are of our astronauts. I want to thank you for being risk takers for the sake of exploration."
The Discovery's commander, Col. Eileen M. Collins, who is retired from the Air Force, replied: "We all enjoy what we're doing. We really believe in our mission, and we believe in space exploration and getting people off the planet and seeing what's out there. The steps we are taking right now are really worth it."
The president finished by saying: "Thanks for taking my phone call. Now get back to work."
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