MANILA — Philippine police have filed rebellion and criminal complaints against the first group of more than 200 rebels and commanders who occupied coastal communities in the south and took residents hostage in a two-week siege that thousands of troops are still trying to quell, prosecutors said Sunday. The first 29 Moro National Liberation Front rebels to face complaints include Habier Malik and three other commanders who remained at large and were reportedly still locked in a deadly standoff with troops in Zamboanga city's coastal outskirts, senior prosecutor Aristotle Reyes said. The other 25 to have complaints filed against them have been captured or have surrendered. Complaints against other Moro rebels, including rebel leader Nur Misuari, will be filed next for allegedly taking part in a rebellion and occupying communities and holding residents hostage in violation of a Philippine law that upholds international humanitarian conventions, officials said. There's “smoking gun” evidence against many of the rebels, Reyes said by telephone. “Many of them were captured during gun battles,” he said. More than 200 Moro rebels, who had arrived by boat from outlying islands, attempted to occupy Zamboanga, a major port city of nearly a million people, but were repulsed by troops on Sept. 9. They then stormed five coastal communities and took about 200 residents hostage as human shields after government forces surrounded them, the military said. When attempts to convince the rebels to surrender and give up their hostages failed, President Benigno Aquino III flew Friday to Zamboanga city, about 860 kilometers (540 miles) south of Manila, to oversee a ground, sea and air offensive by 4,500 soldiers and police, military officials said. At least 102 rebels had been killed, while 117 others have been captured or surrendered. About 40 rebels holding around 20 hostages continue to fight troops in two communities, military spokesman Lt. Col. Ramon Zagala said, adding that troops have used limited firepower to protect civilians. Aquino flew back to Manila on Sunday to help oversee aid to a typhoon-hit northern province and deal with other issues. While troops continued battle the last pockets of rebel holdouts in close-range fighting, Aquino said officials have begun discussing how to rebuild communities devastated by the fighting, which displaced more than 100,000 people. It's the most serious fighting in years between rebels and government forces in the predominantly Roman Catholic nation's south, the scene of a decades-old struggle for self-rule by minority Muslims. The rebel faction involved in the fighting dropped its demand for a separate Muslim state and signed an autonomy deal with the government in 1996, but the guerrillas did not lay down their arms and later accused the government of reneging on a promise to develop long-neglected Muslim regions. Misuari's group splintered into factions and faded into the background while a bigger rival group entered into talks with the government on enlarging an autonomous Muslim region in the south. As the talks brokered by Malaysia progressed, Misuari and his group felt left out and grew restive. Misuari has not been seen since the rebel siege began, but Aquino III has said there was growing evidence of his involvement. — AP