Canadian troops have been searching caves
US General Tommy Franks made the announcement about Operation Anaconda at Bagram airbase, on the outskirts of Kabul.
"It is possible for al-Qaeda and Taleban fighters to regroup in various parts of Afghanistan and that is why we are not saying that this is over. I suspect that this kind of operation could happen again," he said.
US officials estimate 500 fighters have been killed during the offensive in the Shah-i-Kot valley and Arma mountains, south of Gardez. But local Afghan commanders have suggested many of the guerrillas may have escaped into Pakistan.
At least 15 American and Afghan Government soldiers have been killed in the operation.
Valour award
General Franks flew in to Afghanistan on Monday after visits to Pakistan and Somalia.
"Anaconda will be completed within 12 hours because of you," he told some 300 troops at a ceremony where he awarded the Bronze Star to four US servicemen who took part in the operation.
"You did it on time, you did it with a good plan, you did it with violent execution, you did it taking care of one another," General Franks added.
Careful search
The most intense fighting in Operation Anaconda, the largest US-led offensive in the Afghan war, ended on Wednesday.
Since then about 500 Canadian and US soldiers have been working with allied Afghan fighters to search the caves in the mountains near the city of Gardez, about 150 kilometres (95 miles) from Kabul, to flush out any remaining fighters.
Captain Steven O'Connor, a spokesman for the 10th Mountain Division, said the coalition forces had searched about 30 caves so far - finding ammunition, clothing, supplies and sensitive documents.
But they have had no contact with enemy fighters in the past 24 hours and no new casualties have been reported, he said.