After nearly four decades of deadly conflict the Philippines largest Muslim rebel group, the Moro Islamic Liberation Front, has signed a peace treaty with the government.

Malaysia's prime minister Najib Razak attended the historic signing, marking the culmination of his country's role as facilitator in the long and tedious process of negotiations.

For Mohaqar Iqbal, who signed the peace agreement as chairman of the Moro Islamic Liberation Front alongside Philippine president Benigno Aquino, the event was momentous.

"I am relieved substantially because for the last 16 years it has been a very, very hard demonstration between us and the government," he told the ABC.

The peace deal outlines plans to create a Bangsamoro self rule area in Mindanao in Philippines' south.

Autonomous region

The autonomous region will cover about 10 per cent of territory in the majority Roman Catholic Philippines, will have its own police force, a regional parliament and the power to levy taxes.

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Revenues from the region's vast deposits of natural resources will be split with the national government and Manila will retain control over defence, foreign policy, currency and citizenship.

President Aquino's next challenge will be to convince Congress to pass a "basic law" to create the autonomous region before the Comprehensive Agreement on the Bangsamoro (CAB) can be implemented.

And that's not going to be easy according to Jesus Dureza, the former chief government negotiator and the presidential adviser to the peace process in the Arroyo government.

"Because many of those who are in Congress right now, represent also this area, but they are entrenched, the political leaders, and therefore they may resist changes that will affect them," he said.

"So this is very crucial in terms of President Aquino to get the Congress to move very closely to the terms of the agreement.

"Remember we had bad lessons with the Moro National Liberation Front (MNLF) agreement in 1996 when Congress crafted the arm law, many MNLF leaders felt they crafted the new agreement."

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The peace process with the MILF came to a grinding halt in 2008 when the constitutional court threw out the Muslim claim to an ancestral domain.

Despite whispers from some sectors of society that this deal would also be challenged in court, Mr Iqbal is confident that there will be support for the CAB within Congress.

"With the strong partnership between the Government and President Aquino and the Moro Islamic Liberation Front we are very optimistic that all [issues will] be addressed by both parties."

Dissent from the peace deal can also be expected from other armed groups outside of the MILF, groups like the Abu Sayyaf and the Bangasamoro Islamic Freedom Fighters, a splinter group of the MILF.

Steps to peace ongoing

Mr Dureza says for there to be comprehensive peace, the government and the MILF need to address the concerns of the MNLF which had signed a peace agreement with the government in 1996.

"We cannot go forward with MILF peace agreement unless we can get convergence with the MNLF peace agreement because they cover the same area, the same territory and the same people," he said.

"It's very important now that there would be some kind of convergence that would have to be forged with MILF and government together, reaching out to the MNLF.

"Unfortunately over the past period they had been ignored or sidelined."

However, Mr Iqbal says there is direct contact with the MNLF.

"We have a direct engagement with them and we are telling them, this is for our people."

The new Bangsamoro autonomous region will face its greatest challenge in mid-2016 when the Philippines goes to the polls.

Mr Dureza fears that the transition time from now until 2016 maybe too short for the MILF to win the confidence of its electorate.

"They will have to compete now with all politicians the short term transition period may not be enough time for people to be convinced that the MILF can run it properly and in a better way."

It's a challenge Mr Iqbal says the MILF must face.

"We are fully aware of the hardships along the way but there is no other way to do it, except to do it."