Astronaut Stephen Robinson said both pieces came out easily. He did not have to use a makeshift hacksaw that he carried along just in case.
"That came out very easily, probably even less force," Robinson said of the second piece. "I don't see any more gap filler. ... I'm doing my own inspection here. It is a very nice orbital belly."
NASA had said the protruding material on the shuttle could cause dangerous overheating during re-entry and lead to another Columbia-type disaster.
Discovery will remain docked at the space station until Saturday. It's set return to Earth early Monday.
CBS News Correspondent Mark Strassmann reports the repair was considered to be fairly straightforward, and it is one the astronauts have trained for, although they have never actually tried it in space.
CBS News tech analyst Larry Magid speaks with astronaut Buzz Aldrin about the Discovery mission.
The president wished the crew "Godspeed for your mission."
"Thanks for being such great examples of courage for a lot of our fellow citizens," Mr. Bush said.
Discovery Commander Eileen Collins told Mr. Bush, "We really enjoy what we're doing. We really believe in our mission."
Nobody's ever worked under the shuttle before and if you're not really careful you could hit the bottom and do some damage. But CBS News Correspondent Peter King reports Robinson seemed most concerned about something we all worry about during home improvements - hitting his head.
Robinson took only essential tools for the repair - leaving anything else he may need, including a tile repair kit, just outside the airlock. He'll also make sure to secure his safety tethers between his legs and behind him to prevent accidentally striking the vehicle.
Once under Discovery's belly, Robinson was expected to spend about an hour removing or trimming the fillers from two locations near the shuttle's nose.
NASA officials had thought Robinson would be able to easily pull the first gap filler - about the thickness of three index cards bonded together - by using his gloved hand.
"Because of the way this gap filler is sticking up at both ends, it does not appear to be bonded," NASA officials told the crew in uplinked materials. "We expect it to slip out easily."
Once work is completed at the first location, astronauts planned to reposition the station's arm so Robinson could reach the second protruding piece of filler, which sticks out about an inch.
That piece could be trickier, as NASA officials believe it remains glued to a shim that is bonded to a thermal tile.
There are 24,300 glass-coated tiles on the shuttle, a majority of them on its belly. The tiles protect the shuttle from the extreme temperatures in orbit and, more importantly, insulate the ship during launch and re-entry.
The filler material protects the tiles from bumping against one another during launch, but isn't needed for landing because of the difference in the airflow.