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Dismantling GuantanamoClosing down the prison camp may be easier said than done.

By Jonathan MahlerPosted Wednesday, Nov. 12, 2008, at 4:52 PM ET

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But even if these men are eventually released, there will be others that the new administration will want to keep behind bars. For them, one possibility would be for Obama to ask Congress to pass some sort of legislation expanding his authority to detain suspected terrorists for preventive reasons. Another option is prosecution.

It seems safe to say that Obama's preferred venue for trial will be the federal courts. This is the approach many on the left have been agitating for since 9/11. Last May, Human Rights First issued a 183-page report, "In Pursuit of Justice: Prosecuting Terrorism Cases in the Federal Courts," aimed at supporting this argument. As Matthew Waxman, a law professor at Columbia who worked on detainee issues in the Defense Department, notes, the federal courts are now much better-equipped to deal with terrorism cases than they were at the time of the Sept. 11 attacks. In addition to all the resources we have devoted to our federal anti-terrorism infrastructure in those intervening years, our criminal statutes have been revised to accommodate greater liability for conspiring with terrorist groups, and federal judges are now more experienced at dealing with sensitive information.

But there has also been at least one report that Obama is considering an alternative to both President Bush's much-maligned military commissions and the federal judicial system—a newly created system of national security courts. These courts would likely be composed of federal judges with lifetime tenure and would function along the lines of existing specialized courts that deal with complicated issues like bankruptcy.

In a sense, the advantages of prosecuting suspected terrorists in a national security court would be the same as its disadvantages: It would presumably afford more flexibility than a regular federal court for, say, things like the standard of proof for admitting evidence collected on the battlefield in Afghanistan. The idea was first floated in July 2007 in a New York Times op-ed co-authored by Neal Katyal, who represented Hamdan at the Supreme Court, and Jack Goldsmith, a former assistant attorney general in the Bush administration. It has since been widely derided by human rights and civil liberties lawyers (among others) who warn that the creation of such a court would represent a rejection of fundamental principles of American constitutional law—and would, in turn, raise the same legitimacy questions as the military commissions themselves.

On Monday, the Associated Press ran a story, attributed to three unnamed Obama advisers, claiming that he was planning to go forward with a proposal for national security courts. Hours later, though, Denis McDonough, a senior Obama adviser, told CNN that no such decisions had been made. McDonough's correction—or, at the very least, qualification—makes sense. Until President Obama's national security team is in place and has studied the files of the remaining detainees, it's hard to imagine that there will be much progress on the specifics of how to deal with these men.

That day will arrive, though, and when it does, the question will come down to whether the new president feels that he can rely on the criminal-justice system to convict individuals he doesn't want to release. The Human Rights First report justly cites dozens of successful criminal terrorism prosecutions, but it's worth remembering that those were all cases that the Justice Department chose to prosecute in the federal courts.

Obama's flexibility to handle the remaining detainees as he sees fit will be constrained by the manner in which they have been treated while in U.S. custody. Remember that Hamdan was chosen as the first defendant for the military commissions in large part because the prosecution thought it has a "clean" case against him—and yet on the very first day of his trial, his military judge threw out a number of his statements to interrogators, ruling that they had been coerced from him and were therefore unreliable. And that happened in a trial system effectively designed by the Pentagon to ensure convictions.

Look at it this way: Of the 200 or so detainees left on Guantanamo who have not been cleared for release (pending the necessary arrangements), the Bush administration intended to try only some 70 or 80 before military commissions. That leaves more than 100 whom it considered too dangerous to release but was not planning to put on trial. "What lies in those files that's an obstacle to prosecution?" Waxman asks.

When Obama finds out, he may learn that his options for keeping them locked up are limited.