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As the Obama administration contemplates where to try the self-confessed 9/11 mastermind Khalid Sheikh Mohammed and his co-defendants, there could be no better way to repudiate the unlawful counter-terrorism policies of the Bush administration than to hold these trials in New York federal court.

New York is where the crime took place and where the majority of the victims lived. The victims' families have a right to witness these trials and to support firsthand the US government's efforts to hold accountable those accused of this mass murder. And by choosing a federal court over the discredited military commissions, the US would show that it values the rule of law, trying even those accused of the worst crimes in a system that is broadly recognised as fair.

Any verdict by the military commissions will inevitably be tainted by the stigma of Guantánamo, where they are held. As would be expected from a tribunal created from scratch, proceedings there have been marred by endless irregularities, inconsistent application of the rules of evidence, inadequate defense resources, poor translation and lack of public access. As a result, any verdict by the military commissions is extremely vulnerable to appellate challenges - and would delay the finality of justice for the victims for years to come.

Further, justice at Guantánamo has proceeded at a snail's pace compared with trials in federal court. During the nine years since the military commissions were first announced, military prosecutors have completed only five cases, three by plea bargain. Most of these prosecutions have been of low-level offenders - cooks, drivers and even one former child soldier captured when he was only 15.

Federal courts, by contrast, have prosecuted hundreds of terrorism-related offences during the same period, including the 9/11 conspirator Zacarias Moussaoui, the convicted "shoe bomber" Richard Reid, and four defendants in the 1998 US embassy bombings in Tanzania and Kenya, which killed 224 people and injured hundreds more.

As a former prosecutor in the southern district of New York, I know that the experience and professionalism of the federal system - while not flawless - cannot be matched. With a long history of providing fair trials, often in difficult cases, the federal courts can look to decades of binding precedent for guidance. By contrast, the military commission prosecutors and judges have been at it for only eight years, and much of that time, the rules were being adjusted and revised. Their rules of evidence, for example, were finalised only in May. By allowing the military commissions to handle this type of difficult, politically-charged case, the enormous publicity that the trials are bound to draw would likely be more focused on the untested and unfair procedures than on the heinous crimes of the accused.

Some contend that the 9/11 defendants should not be prosecuted in federal court because, then, their coerced statements could not be used against them. It is well-known that Khalid Sheikh Mohammed has been waterboarded approximately 183 times. Evidence derived from such torture should not be used in any court - and both federal courts and the military commissions would bar it. While military commission rules, to their discredit, would allow the admission of some coerced evidence that might otherwise be prohibited in federal court, even the military commissions would never admit statements derived from waterboarding.

Moreover, a review of the evidence already presented against the 9/11 defendants at the military commissions shows that the government probably has plenty of evidence unrelated to abusive interrogation that could be used against them, including computers and cellphones seized, conversations intercepted, and even witnesses who have cooperated voluntarily. We should not assume that coerced evidence is the only evidence prosecutors have to make their case.

Some opponents of holding the trials in New York cite purported security concerns, but these fears are overblown. Large-scale demonstrations and events take place in New York without incident all the time. Federal courts are well-equipped to handle high-profile cases and have done so numerous times in the past.

In fact, the trial of the first former Guantánamo detainee, Ahmed Khalfan Ghailani, transferred to federal court in 2009, is winding down now in downtown New York (the jury is deliberating this week). Ghailani is accused in the US embassy bombings in Tanzania and Kenya. His case has been going on since early October, yet none of the security concerns raised by opponents of holding civilian trials ever arose. Even if these concerns had merit, there are a number of venues other than downtown Manhattan where a trial of this importance could still be held and New York's jurisdiction maintained.

One alternative being floated to federal court prosecutions is the possibility of no trial at all, but rather, indefinite detention without trial until the end of hostilities. That has the obvious disadvantage of being only temporary, since, at some stage, al-Qaida will cease to exist, and the US would then be obliged to release the suspects or hold a long-delayed trial. Far better to try them now when evidence and witnesses are still relatively fresh, and to impose the lengthy prison terms that should attend conviction for such crimes.

Moreover, the war framework is wrong for such awful crimes since it allows the suspects to glorify themselves as combatants. Khalid Sheikh Mohammed has already begun doing so: during a hearing in Guantánamo, he compared himself to George Washington. Only a criminal trial and conviction that fully respects the rights of defence would allow those accused of these heinous crimes to be condemned as despicable criminals - in a way that affirms the values that were so ruthlessly attacked on 9/11.

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