President Juan Manuel Santos, who was Colombia's defense minister when the CIA covert program ramped up, has increased efforts to weaken the FARC. (Jose Cendon/Bloomberg)

Colombia continues to upgrade its air capabilities. In 2013, the air force upgraded its fleet of Israeli-made Kfir fighter jets, fitting them with Israeli-made Griffin laser-guided bombs. It has also fitted smart bombs onto some of its Super Tucanos.

Having decimated the top FARC leadership and many of the front commanders, the military, with continued help from the CIA and other intelligence agencies, appears to be working its way through the mid-level ranks, including mobile company commanders, the most battle-hardened and experienced remaining cadre. One-third of them have been killed or captured, according to Colombian officials.

The Santos administration has also targeted the financial and weapons networks supporting the FARC. Some critics think the government has been too focused on killing leaders and not enough on using the army and police to occupy and control rebel territory.

Killing an individual has never been a measure of success in war, say counterinsurgency experts. It’s the chaos and dysfunction that killing the leadership causes to the organization that matters. The air operations against the FARC leadership “has turned the organization upside down,” said a senior Pentagon official who has studied the classified U.S. history of Colombia’s war.

Some have fled to Venezuela. One member of the secretariat hides out intermittently in Ecuador, according to senior Colombia officials, breaking the important psychological bond with ground troops and handicapping recruitment.

For fear of being located and targeted, units no longer sleep in the same place two days in a row, so camps must be sparser. “They know the government has so much information on them now, and real-time intelligence,” said German Espejo, security and defense counselor at the Colombian Embassy. Worried about spies in their midst, executions are common.

The FARC still mounts attacks — a car bombing of a rural police station Dec. 7 killed six police officers and two civilians — but it no longer travels in large groups, and it limits most units to less than 20. No longer able to mount large-scale assaults, the group has reverted to hit-and-run tactics using snipers and explosives.

The weariness of 50 years of transient jungle life has taken its toll on the FARC negotiating team, too. Those who have lived in exile seem more willing to continue the fight than those who have been doing the fighting, said Colombian officials. The negotiations, Santos said in the interview, are the result of the successful military campaign, “the cherry on the cake.”

On Dec. 15, the FARC said it would begin a 30-day unilateral cease-fire as a sign of good will during the holiday season. The Santos administration rebuffed the gesture and vowed to continue its military campaign. Later that day, security forces killed a FARC guerrilla implicated in a bomb attack on a former minister. Three days later, the army killed another five.

Elyssa Pachico and Julie Tate contributed to this report.