MARIMONDA ALTA, Colombia — After a taxing, three-hour hike into the Sierra Nevada Mountains, Sandra Vargas spotted her family’s abandoned farmhouse — and the makeshift cemetery in the backyard.

It was here, on Jan. 6, 1991, that guerrillas executed her brother, Jose de Jesus Vargas, and ordered their parents to inter him.

Now, accompanied by forensic anthropologists, Sandra Vargas had returned to extract the remains of her brother and give him a proper burial. “I’ve always wanted to do this but never had the chance,” Vargas said as the search team began turning over dirt. “I’ve been waiting for 18 years.”

The waiting is over for legions of Colombians whose loved ones were killed in the country’s 45-year-old war. The ongoing conflict pits leftist guerrillas against government troops and right-wing paramilitary death squads but most of the victims are civilians.

The excavations began in 2005 after thousands of paramilitaries disarmed. In exchange for lighter prison terms, the militia commanders — who ordered thousands of killings — had to confess their crimes and provide information on where the dead are buried.

So far, forensic anthropologists have uncovered the remains of nearly 2,500 people. But their work is just beginning. More than 21,000 noncombatants have been officially registered as disappeared with some cases dating back to 1974.

Other victims were targeted by the guerrillas and the Colombian army. In fact, there are so many pending cases that the government’s 15 teams of forensic anthropologists have narrowed their focus to sites where they have a clear idea of the identities of the dead in order to return the remains to relatives.

“For the families, it helps bring closure,” said Fernan Gonzalez, a Roman Catholic priest and a member of a government-appointed reconciliation commission that is putting together a history of the war.

Unlike similar efforts in Bosnia, El Salvador, Guatemala, Peru and Argentina, which were carried out once the hostilities had largely ended, some of the excavations in Colombia are taking place in active war zones.

As a result, the search parties must embed with Colombian Army troops who search the area for guerrilla and paramilitary units then set up a security perimeter.

Some team members are a little surprised at their line of work.

After earning a university degree in anthropology, Juliana Lopez figured she’d spend most of her time uncovering ancient ruins at archaeological sites. Instead, she’s getting a crash course in Colombia’s more recent — and tragic — history.

To locate the remains of Jose de Jesus Vargas, who was killed by a now-defunct Maoist guerrilla group known as the Popular Liberation Army, Lopez and two other anthropologists were joined by Sandra Vargas, the victim’s sister, who knew where her brother was buried and served as their guide.

Sandra, who was only 6 when the crime occurred, has no idea why the guerrillas executed her brother, who was 24. But in many cases, civilians are targeted for allegedly collaborating with the enemy. After the killing, the Vargas family fled the area and Sandra was returning to the farm for the first time in years.

The day began at 3 a.m. when she met the search team in the coastal city of Santa Marta. After picking up a squad of soldiers, they drove into the Sierra Nevada Mountains, which jut dramatically out of the mostly flat landscape along Colombia’s Caribbean coast. Their craggy peaks and valleys have long provided refuge for guerrilla and paramilitary groups. Thus, when the road petered out and the long march began, the soldiers fanned out to clear the way.

Reaching the grave site was half the battle. The anthropologists loaded some of their gear onto the back of a rented mule but as they crossed streams and negotiated the winding footpath, they were soon sweaty and exhausted.

They reached the Vargas farm at 1 p.m., and had to work fast. Guerrilla groups were in the area so instead of camping overnight, the team had to find the body and get back down the mountain before darkness set in.

Mosquitoes and gnats filled the air and the forest floor was alive with biting ants. But the search team paid no attention. Sandra indicated the spot where she thought her brother was interred and the anthropologists began jamming a metal probe into the ground.

After a few false starts, they detected a soft spot, indicating that the soil had been moved. When they removed the top layer of dirt, they noted that the underlying soil gave off a reddish hue. The change in color, they said, was due to a chemical reaction, likely caused by the decomposition of bones.

They were getting closer.

Now lying on their bellies, the anthropologists switched from shovels to trowels for the delicate work that lay ahead. Soon, they found a rotten length of belt and then a ragged pair of underwear. Next, they spotted something black and shiny: a rubber boot with a grey shin bone sticking out of the top.

Sandra took a deep breath. The team had found her brother.

“Now he is with us again,” she said.

After photographing rib, femur and finger bones, the anthropologists placed the remains in plastic bags, taped them shut, and slung them onto the back of the mule. The bones would eventually be transferred to a government laboratory for DNA testing then returned to the family for the last rites.

Mission accomplished, the soldiers and the anthropologists began the long slog back down the mountain. And because so many clandestine graves have yet to be excavated, they were up before dawn the next day to set out on another dig.