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Right now there are two places to try terrorism suspects - criminal courts and military commissions at Guantanamo Bay, Cuba. Later this year, the biggest terrorism trial to date will take place at Guantanamo. It's the military trial of the alleged September 11 conspirators. The problem is these commissions haven't been seen as legitimate. NPR's Dina Temple-Raston reports on the Obama administration's effort to change that perception.

DINA TEMPLE-RASTON, BYLINE: There's already one case underway at Guantanamo. It involves the man accused of masterminding the attack against the USS Cole in Yemen in 2000. His name is Abu al-Rahim al-Nashiri. While he's being tried in a special courthouse at Guantanamo, there's something unusual about his case. Some of the lawyers on the team prosecuting him aren't from the military at all. They're from the Justice Department.

LISA MONACO: Right now we've got eight full time prosecutors that are assigned to the active and pending cases in the military commission system, so that would be the Cole case and the 9/11 case.

TEMPLE-RASTON: That's Lisa Monaco, the assistant attorney general for National Security at the Justice Department. And she says that for all the debate about whether to try terrorism suspects in military commissions or civilian courts, a very important detail got lost. The military commissions system has been reformed. And in large part it's been modeled on federal courts in this country. That's one reason why the people arguing these cases aren't just military attorneys anymore. They're criminal lawyers.

MONACO: We've got folks who are spending full time down at Guantanamo. We've got lawyers who are spending time in court, as they did last week in the Nashiri case. So they're participating fully, both at Guantanamo and back in the States.

TEMPLE-RASTON: Those Justice Department lawyers are working for this man.

BRIGADIER GENERAL MARK MARTINS: I'm Brigadier General Mark Martins, and I am the prosecutor of military commissions.

TEMPLE-RASTON: General Martins has been called Guantanamo's detox man. His mission: provide legitimacy to the detainee trials. And that's a difficult task. He's the sixth person to get the chief prosecutor's job in seven years. One chief prosecutor was accused of rigging the process to ensure convictions. Another one left saying he was pressured to include evidence derived from torture in a commission proceeding. General Martins says military commissions are different now. They're fair.

MARTINS: Law is being applied, judges are interpreting laws, counsel are arguing for different pieces of a particular motion, and justice is being done. And we're just absolutely committed to that.

TEMPLE-RASTON: The military commission and federal court system are seen as close enough now that criminal lawyers can work within the military commission's rules to try a case. Matthew Waxman, a professor at Columbia University who used to be in charge of detainee affairs in the Bush administration, says there's a lot at stake here.

MATTHEW WAXMAN: The Obama administration wants to show that the new and improved military commissions are a fair, a legitimate and effective option.

TEMPLE-RASTON: Not everyone is convinced. Even with the Justice Department lawyers sitting at the prosecution table at Guantanamo, critics still have reservations about the military commissions. For example, it's difficult for defense attorneys to represent their clients. The logistics of getting to Guantanamo make it hard for lawyers to meet with the defendants. And there are strict security rules that make communication difficult.

Another concern: Detainees don't have the right to confront an accuser if that accuser is an unnamed intelligence agent. General Martins acknowledges that the two systems are not identical. But he says both the military commissions system and the federal courts have a place in trying terrorism suspects. It isn't just one or the other.

MARTINS: This all or nothing choice that is sometimes portrayed between a law enforcement approach and a military approach is a false choice.

TEMPLE-RASTON: The big test for military commissions could come as early as April. That's when Khalid Sheikh Mohammed and the other alleged 9/11 plotters are expected to be arraigned. General Martins hasn't picked a lead prosecutor for that case. He wouldn't rule out that a Justice Department lawyer could be sitting in the first chair.

Dina Temple-Raston, NPR News.

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