Two former Border Patrol agents arrested on charges of smuggling Brazilians and Mexicans into the country on Friday made their first appearance in U.S. Federal District Court in San Diego.

The Associated Press reports that a U.S. magistrate judge entered not guilty pleas on behalf of brothers Fidel, 41, and Raul, 39, Villarreal, as uniformed Border Patrol agents looked on disapprovingly at their former co-workers. The brothers, who were extradited from Mexico on Thursday, had been on the lam for more than two years until their arrest last October in Tijuana. Since then the men had been held in Mexico City pending their extradition to the United States.

A federal grand jury in April indicted the brothers on 18 counts of bribery, alien smuggling, money laundering and witness tampering, but the indictment was sealed until after their arrest in October.

The Villlarreals were allegedly part of a network that smuggled Brazilians and Mexicans into the country through Tijuana, according to court documents. The network included a Mexican police officer who drove the immigrants to remote mountain areas from where the brothers would drive them in a Border Patrol truck further into the country, a Brazilian said in a sworn affidavit, adding that he paid $12,000 to be smuggled into the country.

The brothers, who were highlighted in a joint New York Times-PBS Frontline/WORLD production in May 2008, were assigned to different Border Patrol posts in the San Diego area. Fidel Villarreal was a senior agent while Raul Villarreal was once a Border Patrol spokesman, who acted as a “coyote” in public service announcements for the Mexican government warning immigrants about the dangers of human smugglers.

The brothers were captured during an early morning raid following a birthday party at a gated apartment complex near the U.S. Consulate. Their father, who lived near the border in National City, Calif., was also at the apartment at that time. Two other suspected smugglers, Armando Garcia and Claudia Gonzalez, who were caught along with the brothers, were also extradited.

The brothers had lived with their parents in a San Diego suburb until they abruptly quit the Border Patrol in June 2006 and vanished. Federal agents involved in the investigation speculated that the brothers may have been tipped off about the investigation as it closed in on them, and had chosen to go into hiding.

Jan E. Ronis, the attorney for Raul Villarreal, declined to comment on his client’s case beyond the fact the brothers are in a difficult position.

“Obviously the allegations are serious,” he said.

Andrew Becker is a reporter for Reveal, covering border, national and homeland security issues, as well as weapons and gun trafficking. He has focused on waste, fraud and abuse – with stories ranging from border corruption to the expanding use of drones and unmanned aerial vehicles, from the militarization of police to the intersection of politics and policy related to immigration, from terrorism to drug trafficking. Becker's reporting has appeared in The Washington Post, the Los Angeles Times, The New York Times, Newsweek/The Daily Beast and on National Public Radio and PBS/FRONTLINE, among others. He received a master's degree in journalism from UC Berkeley. Becker is based in Reveal's Emeryville, California, office.