But another significant, and so far less widely discussed, issue is coming to the fore - if and when peace is achieved, what role can or should the Colombian military play?
Much of the focus to date has seemingly been around the possible demobilisation of the several thousand Farc (Revolutionary Armed Forces of Colombia) rebels who have been fighting the Colombian state for almost five decades.
"People are talking about the demobilisation of the Farc," retired Col Hugo Bahamon told a recent seminar of academics and high-ranking officers at Bogota's Military Club.
"But if a peace agreement is reached, we need to think about the demobilisation of many members of the armed forces as well."
Currently there are an estimated 400,000 serving military personnel in Colombia.
What would peace mean to them?
The Colombian armed forces are looking for protection from what could potentially happen if a post-conflict Farc were to become a legitimate political force and enter mainstream national politics.
Ballots
Speaking at the same meeting, Armed Forces Commander Gen Alejandro Navas said: "They [the Farc] have the objective of winning the national elections in 2018. The presidential elections in 2014 are just a test and then they will be unstoppable at the ballots if there are no solid political parties."
Whether the Colombian electorate would back a Farc party to the degree Gen Navas fears may be disputed.
But military men like him and Col Bahamon are clearly concerned, particularly as serving members of the armed forces do not have the right to vote.
They are worried that members of the security forces may end up in the dock.
In such a long-running conflict, atrocities have been committed by the guerrillas and the armed forces.
If - and it is a big if - the rebels benefit from amnesties, will the same be true for the armed forces?
Col Bahamon expressed fears that even if amnesties are in place for the security forces, the situation could change.
"Look at what has happened in Argentina and Chile, where, 20 years on, the guerrillas who threatened the state are in power, amnesties have been overturned and now [former soldiers] of 70 and 80 years of age are being imprisoned," he said.
"Why can't we get the right to vote, after all we have been defending the country and fighting for her for 60 years?"
Without the right to vote, members of the military feel they have no judicial security from potential lawsuits.
Hearts and minds
In a law passed earlier this year that sets out the framework for peace, one highly controversial clause was to try the military in civilian courts rather than military tribunals. This is yet to be resolved.
One key element of the debate is whether the Farc rebels are still militarily powerful or more of a political entity.
Lt Col Laureano Novoa, a leading intelligence expert, recalled that the last time peace talks were tried, and failed, the Farc held the upper hand.
"This time around they are not making the rules," he said.
But Ronald Archer, a special adviser to the US Army, believes that the Farc as a movement has significant power due to its political activities - and that is why the army must do more to improve its own relations with the civilian population.
""The Farc's support is concentrated in rural areas, which have been subjected to years of indoctrination," said Mr Archer.
"Their declarations that the Colombian State has abandoned these hard-to-reach lands must be exposed through showing the people the benefits of a state presence."
The agenda for the peace talks includes agrarian reform, recognising the rights of the victims of the conflict and accepting the political legitimacy of opposition movements that may emerge in the wake of a peace deal.
It is set to be a long road, but if peace does come, it will herald many changes in a country marked by conflict for the past 48 years, which has seen more than three million people displaced by the violence.
But should the Farc demobilise, there will be a potential power vacuum in some parts of Colombia.
There is a fear that well-trained members of the military, like demobilised paramilitary fighters before them, could enter the rank and file of the "Bacrims", the illegal criminal bands involved in drug trafficking and extortion.
And while Farc rebels may be ready to give up their fight against the state, it is unclear how many will opt to remain involved in the illegal drugs trade.