The anti-Taleban Afghan forces, backed by US and British troops, have taken dozens of prisoners since Sunday as they have cleared areas in Tora Bora.
But the BBC's correspondent in Tora Bora, Damian Grammaticas, says that anti-Taleban forces are still meeting with resistance from pockets of al-Qaeda fighters.
Many of al-Qaeda fighters have fled to the higher hills and the bombing by US planes is continuing.
Bin Laden still missing
Al-Qaeda bases in the region fell over the weekend following a sustained bombardment by US warplanes.
But despite allied gains on the ground, few senior al-Qaeda figures have been captured.
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There is still no sign of their leader, Osama Bin Laden, the man accused of masterminding the 11 September terror attacks on the United States.
Speaking at the Pentagon, Rear Admiral John Stufflebeem said Bin Laden's whereabouts were anybody's guess.
The anti-Taleban forces have been searching the network of caves and tunnels in Tora Bora to flush out any remaining fighters, while other troops have been stationed on mountain ridges to cut off possible escape routes.
But the search has been complicated by the inhospitable terrain and the presence of mines.
Mr Stufflebeem said the search for al-Qaeda fighters in the Tora Bora was a difficult job.
"I guess maybe searching for fleas on a dog is one way that I would think of it. If you see one and you focus on the one, you don't know how many others are getting away," he said.
On the run
US Defence Secretary Donald Rumsfeld says that as many as 2,000 al-Qaeda fighters, many of whom come from outside Afghanistan, are still on the run.
Hazrat Ali, who is leading the anti-Taleban Afghan forces in the area, said 200 al-Qaeda fighters had been killed and 35 captured.
The BBC's Damian Grammaticas in Tora Bora says that on the ridges where the al-Qaeda caves have been captured, fires are still burning, trees have been smashed, shredded clothes and shrapnel are strewn on the ground.
Captured al-Qaeda fighters were led down the mountainside pleading with their captors not to hand them over to the Americans. Some were in tears.
One group of prisoners is being held in a small mud-walled compound at the base of Afghanistan's White Mountains, our correspondent says.
Battered down
About a dozen, some of them Arabs, were led out and put on show.
They begged their captors not to parade them in public, and said they would rather be shot than degraded in this way.
Some of the men were bandaged and limping, others looked exhausted, filthy and tired.
One prisoner said he was in a group of 60 al-Qaeda members, half of whom had been wiped out in a single US bombing raid.
One Yemeni man who surrendered said he had seen Bin Laden in the area 10 days ago.
Troops from neighbouring Pakistan are controlling the Afghan border to prevent al-Qaeda members or Bin Laden from slipping across, but there have been several reports that the al-Qaeda leader may already have done so.
Bartering for freedom
There have been reports that some Taleban and al-Qaeda fighters who had been in the custody of opposition forces have managed to negotiate their freedom.
"This country [Afghanistan] has a history of bartering and allegiances can be bought, so we suspect that that, in fact, has been happening," Mr Stufflebeem said.
US Secretary of State Colin Powell has trumpeted the Tora Bora conquest as the virtual destruction of al-Qaeda within Afghanistan.
But he also indicated that the war against terrorism is far from over.
"Al-Qaeda is being destroyed in Afghanistan. Now we have to destroy it wherever it exists around the world."