Johnny Sutton isn’t everyone’s favorite federal prosecutor.

President Bush’s pick for U.S. Attorney for the Western District of Texas, confirmed by the U.S. Senate on Nov. 30, 2001, has been vilified in the media and by Border Patrol groups, a few lawmakers and others for his prosecution of several U.S. Border Patrol agents.

On June 30, the San Antonio and Austin Chapters of the Minuteman Civil Defense Corps. and hundreds of bikers from American Freedom Riders — a group dedicated to stopping illegal immigration from coming across the border — will surround Sutton’s office at high noon and call for him to resign.

"The U.S. Department of Justice provides injustice under the leadership of Attorney General [Alberto] Gonzales, while allowing U.S. Attorney Johnny Sutton to protect dopers illegally here, while betraying and preying on young children and violating their civil and human rights," said Andy Ramirez, chairman of Friends of the Border Patrol.

But Sutton, 46, insists his office is not out to put Border Patrol agents or other law enforcement officers behind bars, and he wants to set the record straight.

"There’s nothing a prosecutor desires less to do than to prosecute a cop or federal agent. These are our friends, these are our co-workers. We see the heroic efforts they make. But when they commit crimes, they need to be held accountable just like everyone else," Sutton told FOXNews.com in an extensive interview.

He added: "We know how dangerous their job is, we know they make split-second decisions …juries are very deferential to the hardships and difficulties of that job. That’s why it’s so rare you see police officers being prosecuted."

It is, however, up to prosecutors to decide whether to try cases in the first place, and Sutton's opponents say he could have opted not to prosecute some of these cases, or at the very least, could have kicked them down to state courts for lesser sentences.

One case in point — the joint prosecution of former Border Patrol agents Ignacio Ramos and Jose Compean for the February 2005 non-fatal shooting of Mexican drug runner Osvaldo Aldrete Davila. A jury convicted the agents in March 2006 of violating federal gun laws and attempting to cover up the shooting.

Click here to read about Congress' probe into the prosecutions.

The two are serving 11 and 12 years, respectively, in federal prisons. Their cases are under appeal, but in the meantime, they've been in prison since Jan. 17. Ramos was beaten by other inmates shortly after he began his incarceration.

Supporters have argued Ramos, 38, and Compean, 28, were just doing their jobs, but Sutton says there’s more to the story. A jury found Compean and Ramos guilty of shooting at Davila as he was running away, making false reports about the shooting and picking up the bullets in an attempt to cover-up the incident.

"That’s very damning evidence that they know that is not a good shoot. Otherwise, there’s no reason in the world not to say ‘Hey, we just arrested a drug runner with 750 pounds of drugs and he tried to shoot on us,’" Sutton said.

Sutton, whose assistants Debra Kanof and Jose Luis actually conducted the court case, pointed out that federal sentencing guidelines regarding gun use mandates 10-year-sentences for the shooting.

He denied charges that he was overzealous and noted that since he’s been on the job, Border Patrol agents have shot at illegal immigrants 14 times while on duty.

In all those cases — except that of Ramos and Compean — the agents came forward, explained why they used deadly force, why they shot their gun, he said. None has been charged. In four of those cases, illegal immigrants were actually killed.

Justice Served Or Overzealous Prosecutor?

Sutton has also come under fire for prosecuting Border Patrol agent Noe Aleman, who last week reported to a federal prison to serve a one-year sentence.

The 10-year Border Patrol veteran was convicted of harboring and helping illegal immigrants after trying to adopt his wife’s nieces from Juarez, Mexico, as their daughters. The Alemans were approved for the adoption on April 23, 2004. Aleman argues that he reported to federal authorities what he thought was a typographical error on the girls’ visas that said they had only one business day to stay in the United States. He was later arrested and charged with trying to smuggle the girls into the United States. The girls were deported

Aleman says he got bad legal advice about whether the girls could stay in the country and the paperwork needed for that. Sutton counters the idea that a mere "paperwork error" by Aleman sent him to prison.

"If it’s a paperwork error, how come a West Texas jury that’s sympathetic to Border Patrol would convict him of any crime?" Sutton asked. "Instead, he was breaking (laws) and telling lies and falsifying information."

The decision by the U.S. Court of Appeals for the Fifth Circuit upholding Aleman’s conviction cites evidence that Aleman lied about turning in parole forms when the girls returned to Mexico; that he and his wife lied about the girls living in their home; and that he lied to border officials about the girls’ location in Mexico.

All that was "sufficient for a rational jury to find beyond a reasonable doubt that Aleman knew that the aliens were in the United States illegally and to establish criminal intent," the court said.

Then there’s the case of ex-Border Patrol agent Gary Brugman, who while stationed at Eagle Pass, Texas, on Jan. 14, 2001, helped other agents chase down a group of illegal immigrants. When the agents caught up to those fleeing, they ordered them to sit down. Brugman says not all of them were complying and he worried some they may have tried to attack the other agents.

"I ran up to the aliens and with the bottom of my foot I pushed the first alien to the ground (later identified as Miguel Angel Jimenez-Saldana) to the ground and told him to sit down as I said "sientense," Brugman wrote in a Web log about his encounter. "I then turned to a second alien and pushed him to the ground too."

On Feb. 22, 2001, Brugman had a physical altercation with a convicted drug smuggler while responding to a possible narcotics run. During the fight, the immigrant tried to grab his handcuffs while his arm was pinned behind him, Brugman alleges.

"I then punched him in the face three times until he said to me ‘Okay officer, stop hitting me.’" Brugman wrote. "I stopped and told him ‘Then stop fighting!!!" Other agents soon arrived, the man was transported away and later imprisoned.

Click here to read Brugman’s Web log.

On March 15, 2001, Brugman was relieved of his weapon. On Aug. 21, 2002, he was indicted for violating the civil rights of Jiminez-Saldana during the first incident and in April 2004, he was sent to prison for two years.

Sutton notes that several other Border Patrol agents testified that they saw Brugman kick or hit at least one of the aliens. As to claims that one agent was coerced into testifying against his colleague, Sutton said: "If there’s evidence of that, let’s see it … there was no evidence that that agent was coerced. ... That agent was very cooperative."

Sutton noted that the two-year sentence is also mandated by federal law and that the career prosecutors in his eight offices in Texas are professionals who are not out to ruin Border Patrol agents.

"They’re motivation is to follow the law and to make sure justice is done," Sutton said. "They use that discretion day in and day out in a very appropriate way. The great irony in some of this criticism is Border Patrol are our witnesses. They work with us day in and day out."

Then there’s the case of Edwards County, Texas, Sheriff’s Deputy Gilmer Hernandez, who was paid $20,000 a year to help keep watch over the city of Rocksprings, Texas, where the battle with illegal immigrants is a daily one.

On the night of April 14, 2005, Hernandez stopped a speeding Suburban that ran through a red light. As he walked to the driver's side, he said, the vehicle peeled away, almost running over his foot. Hernandez fired several shots, one of which blew out a rear tire. Eight or nine people jumped out of the vehicle and ran off, but one woman who had been hit in the mouth by some of the bullets remained.

Hernandez reported the incident and he was investigated. Prosecutors say that because the agent's life was not in danger, he shouldn't have shot at the vehicle. On Dec. 1, 2006, he was convicted by a jury and sentenced to 266 days in prison, including time served; federal sentencing guidelines could have put him away for 10 years.

Sutton said in all of these cases, his office looked at the evidence and first determined if a crime was committed, then used its discretion to determine whether bringing federal charges against the defendant was the "right thing to do." The other option was to refer the case to state prosecutors for lesser sentences.

"They should be given the benefit of the doubt and believe me, they are. But when they shoot at unarmed people and cover up and file false reports, you cannot look the other way," Sutton said.

"I feel very strongly that one of the reasons America is such a great country and so stable and solid is because we enforce the rule of law, we believe the rule of law. We solve our problems, not in fist fights and mob attacks, but in courtrooms and juries and reviews. No one is above the law in this country," he added.

Sutton has also taken flak because of his closeness to President Bush. He previously served as an associate deputy attorney general at the U.S. Justice Department and as a policy coordinator for the Bush-Cheney transition team. He was the criminal justice policy director for Bush when he was Texas governor from 1995-2000. He currently is chairman of the attorney general’s committee that helps formulate and carry out priorities for the department and the president.

Coziness aside, "there’s zero pressure" to prosecute these cases one way or the other, Sutton said.

"There is no pressure but there are priorities. Presidents and attorneys general have priorities and those priorities may change from administration to administration. Generally, they do not because no matter who is in power, we’re going to enforce the laws."

Despite being a whipping post for groups advocating stricter illegal immigrant laws and more protections for Border Patrol officers, Sutton is philosophical about the criticism he has received.

"It is a job that involves conflict, it involves trials, it’s a very satisfying job because you get to stand up for victims and you get to wear the white hat. But sometimes, unfortunately, you have to prosecute cases you don’t want to prosecute because they’re cops or they’re people you might like," he said.

"But when they commit crimes that are serious crimes, the rule of law is more important than what is going to cause you stress or what is going to end friendships. If prosecutors decide, like some agents, they’re going to enforce laws and not others ... it’s the breakdown of the system."