Every weekday, Juan Andres drives across the U.S.-Mexico border from his home in Ciudad Juarez, Mexico, to the University of Texas at El Paso.

The three-and-a-half-mile commute takes him a world away from a major flashpoint in Mexico's drug cartel war, away from a city with one of the world's highest murder rates.

Andres, who agreed to speak to CNN under the condition that his name was changed, has always been keenly aware of his and his family's safety while living in Juarez.

"The city was already pretty dangerous. We tried not to go to restaurants and things like that where [kidnappings] could happen," he said.

A few years ago, Andres walked away from his career as an optometrist in Mexico to follow his passion: music.

"It was not a hard decision because music is something that I always wanted to do," said the father of two, who is in his 30s.

To expedite his commute to the University of Texas at El Paso, where he studies music education, Andres received a special pass from U.S. Customs and Border Protection after passing a rigorous background check. Applicants have their fingerprints taken and must complete an in-person interview with a Customs and Border Protection officer. They cannot have any previous criminal history.

The SENTRI (which stands for Secure Electronic Network for Travelers Rapid Inspection) pass allowed Andres to waive the standard vehicle check at the border crossing. Most of the time, the border guards just peered inside his vehicle and waved him through.

Authorities were certain that he posed little to no risk of bringing drugs or weapons across the border. What they didn't know was some of these special pass holders, including Andres, were being targeted by Mexican drug cartels, officials say.

"It was a nightmare, like suddenly being in a nightmare," Andres said. "I [asked] God, 'Why did you allow something like this to happen?' "

'I knew it wasn't right'

Living across the U.S. border in Ciudad Juarez, Andres knew the dangers of getting mixed up with drug cartels. He says he did his best to avoid them, staying away from malls and crowded areas where cartels are known to scout potential victims.

"I was working and studying a lot, so I didn't have a lot of free time," he said about his life before last fall.

In Ciudad Juarez, mutilated bodies are often left as warning signs to rival gangs. Despite a recent dip in the homicide rate, many residents still live in fear as police seem virtually helpless.

On the morning of November 16, 2010, Andres drove his 2007 Ford Focus to the Stanton Street Bridge border crossing as he'd done every day for years.

On that day, Customs and Border Protection agents singled him out for a random search and discovered two bags of marijuana in the trunk of his car. He told the agents he had no idea how the drugs got there, but because there was no evidence that his trunk had been tampered with, he was arrested and detained.

"I knew it wasn't right, I didn't know what it was" he says, referring to the two black duffel bags agents found. "I was so afraid. ... All I was thinking was, 'How could that happen?' I had no clue."

Andres was held on the U.S. side of the border in isolation, and interrogated.

"I was afraid of what could happen to my family. I was trying to figure out who could've done that, and nothing came to my imagination. We really didn't have enemies or knew people who were involved in that," he said, referring to the marijuana. "I wasn't working, was completely dedicated to school, my routine was going to school, coming home and doing homework."

Hours later, Andres was able to call his brother, who then called his wife.

"She was scared. We didn't know who did it, so we needed to get my wife out of the house," he said.

Andres' wife took their two young girls and went to stay with his brother in the United States while they waited to hear her husband's fate.

Six months in jails

SENTRI pass holders can use dedicated lanes when crossing the border and have to comply with specific requirements, including an empty trunk.

Andres says he was certain there was nothing in his trunk when he headed across the border last year.