Philippine forces have secured most of the villages earlier captured by rebels, as days of fighting eased in the southern port city of Zamboanga, government officials say.
Authorities said on Thursday that troops had regained about 80 percent of the lost ground in battles with the Moro National Liberation Front (MNLF), which have left 107 people dead.
As the siege in Zamboanga entered its 11th day, the military said one more soldier had been killed and 15 more MNLF fighters had surrendered.
The group objects to a deal signed last October aimed at ending 40 years of conflict and are trying to derail it.
An army spokesperson said troops had begun to conduct clearing operations in the recovered villages in the hope of finding more trapped civilians and securing the area.
About 30 to 40 rebels remained in hiding with 21 hostages in two communities, authorities said.
"We have successfully contained the rebels and can only operate on a very limited area," the Interior Secretary Mar Roxas said.
"If something were to happen outside, these are the ones who were either escaping or who tried to break the area of operations."
Early on Thursday, a gunfight erupted between government forces and retreating rebels, leaving several houses burnt and two rebels killed, officials said.
They said the fighters were fleeing from Zamboanga and heading to outlying islands, off the main southern island of Mindanao.
Isabelle Climaco, Zamboanga city's mayor, appealed to the remaining rebels to surrender.
"Charges shall be filed and justice will be gained for those whose lives were wasted in these atrocities," Climaco said.
Roxas said 96 rebels who had been arrested or surrendered to authorities would be charged under Philippine laws.
"We will file rebellion charges during the inquest proceedings, which will include the specific acts of murder, arson, illegal possession of firearms among other acts," he said.
The fighting has displaced more than 109,000 people and hundreds of homes, and several public and commercial buildings have been destroyed.
Four decades of conflict in the south have left 120,000 people dead, displaced two million and stunted growth in the poor but resource-rich area.