Besides its own challenges, the region must address the economic and trafficking problems.
Mali's new president, Ibrahim Boubacar Keita, will have to overcome huge challenges to bring lasting peace and economic development to his country.
Experts warn that, following a successful French military intervention to drive out armed Islamist militants from the north of the country, the deep-seated and historical conflicts between groups in Mali still pose a threat to stability. A regional approach will also have to be put in place to patrol borders and root out drug trafficking in the vast Sahara desert.
Meanwhile, the African Union is soliciting funds from African countries, including South Africa, to beef up its presence in Mali and assist with the country's reconciliation.
Keita, who was elected with a large majority following a coup d'état in March last year, was inaugurated at a lavish ceremony in the capital, Bamako, on September 19.
It was attended by a wide array of regional leaders, including Ivorian President Alassane Ouattara, President Idriss Deby of Chad and Morocco's King Mohammed VI – and from further north, French President François Hollande, who was given a hero's welcome with shouts of "Merci la France" ("Thank you, France") from the crowd. He said that together French and Malian soldiers had "won the war, chased away the terrorists and secured the north".
But although the main towns of Timbuktu, Gao and Kidal in the extreme north have been liberated from occupation by the armed groups, negotiations are still continuing for a final peace agreement with those who agreed to co-operate with the government. This follows the Ouagadougou agreement signed with the National Movement for the Liberation of Azawad (MNLA) in June.
Lori-Anne Théroux-Bénoni, senior researcher at the Institute for Security Studies' office in Dakar, Senegal, said many of the al-Qaeda-linked groups that were part of the occupation in Mali have fled to the south of Libya. Some have carried out attacks in neighbouring Algeria and Niger.
The lack of exact figures from the French military about how many combatants were killed or captured makes it difficult to gauge the threat against Mali and the region.
"The French say they've broken their backs but we don't have the figures," said Théroux-Bénoni. "What we do know is they have managed to move around and reorganise. We also know that those who were part of Mujao [the Movement for Oneness and Jihad in West Africa] simply melted into the population in Gao."
It is now up to the newly created United Nations Stabilisation Mission for Mali (Minusma) to root out the remaining terror cells. In practice, the mission is the placing of the African-led International Support Mission for Mali (Afisma), which is made up of regional troops, under UN command. The force struggled to get off the ground earlier this year, prompting the interim government to call on France to intervene.
Many Africans are still unhappy about the fact that African forces, though mandated by a resolution of the UN Security Council on December 20 last year, were not given the financial resources to deal with the crisis in Mali on their own. This is creating tension within the mission that could jeopardise its operations.
"If we were given the logistics, we could have liberated Mali without France," a regional source in Bamako said this week. The AU is represented in Mali by former Burundian president Pierre Buyoya, who has a small staff of about 20 AU officials to assist Mali with reconstruction.
Many still blame the United States for not agreeing to a UN resolution that would include financing Afisma, the International Crisis Group, a Brussels-based think-tank, said.
"The African diplomatic community's unanimous approval of the French intervention was accompanied by frustration and even shame at having to rely on their former colonial power to avoid a disaster for the second time in two years," it said in a report on Mali.
According to Théroux-Bénoni, the UN was reluctant to agree on "re-hatting" (redeploying troops with different hats or uniforms) the African-led mission. The task in Mali at this stage is counterterrorism, similar to what the African Union Mission in Somalia (Amisom) is dealing with.
"The UN has always been very careful not to engage in this kind of mission for various doctrinal reasons but also because the UN will never be able to assume the kind of casualties that Amisom has suffered," she said. "There was a lot of tension and questioning before the setting up of the UN force."
According to the resolution authorising Minusma, it is expected to secure major cities and towns in Mali, while a parallel force, led by France, is authorised to deal with "offensive action and emergencies", she said.
Despite the fact that Mali needed France to intervene militarily, the resolution of the problem in Mali could be seen as an example of strong regional co-operation. Shortly after the crisis started, the Economic Community of West Africa (Ecowas) intervened and the strong presence of leaders at Keita's inauguration testified to their continuing support.
Théroux-Bénoni said many countries in the region were "traumatised" by what happened in Mali.
"Many states, especially those in Ecowas, had the feeling that what happened in Mali could easily happen with them," she said. "They have the same problems concerning economic and political governance, with armies that are falling apart. They realise that they wouldn't have been able to handle the same kind of situation Mali faced."
Regional co-operation will be essential, especially to root out the trans-Sahara trafficking routes that have plagued Mali and its neighbours for years. Countries have put into place what is called the "Nouakchott process", following a meeting in March this year to exchange views on terrorism and trafficking.
Experts agree that reconciliation will be a crucial challenge for the new government, not only between the north and the south but also within the army and communities that are severely fragmented.
The Touareg groups in the north, for example, are divided along clan lines and have split into various groups since the start of the occupation last year.
Keita has set up a new ministry for national reconciliation and development of the north, which has promised to organise a national conference to discuss unity.
The AU has promised to assist, using examples from other countries and encouraging the media to play a positive role in nation-building.
The international community has promised up to $3-billion to help to rebuild Mali but analysts agree that this must be used correctly.