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Friday marked a year to the day since Obama signed an executive order pledging to close the controversial detention facility located on the US naval base at Guantanamo Bay, on Cuba's southern tip.
But since then, his administration has struggled to repatriate detainees cleared for release, or find third countries to offer them asylum.
It also took government lawyers longer than expected to process those detainees who would not be released into three categories: those who would be tried before civilian courts, those to be prosecuted by military tribunals, and those who would be held indefinitely and without trial.
On Friday, the administration took one step closer to bringing some of Guantanamo's highest-profile detainees, five men accused of plotting the September 11, 2001 attacks, before a court in New York.
The Pentagon said it had withdrawn charges against the men that were filed before a Guantanamo military tribunal, clearing the way for charges to be filed at a New York civilian court instead.
"This action is a procedural step, which is part of a normal process when an alternative forum is chosen," the Pentagon said.
The five men, including the self-described mastermind of the attacks, Khalid Sheikh Mohammed, are currently being held at Guantanamo, but are to be transferred to New York for trial.
Obama's decision to prosecute the men before a civilian US court rather than a military tribunal has come under fire from Republican lawmakers and some relatives of those killed in the attacks.
But others have praised his administration's decision to accord the men rights as defendants in a civilian trial.
The announcement came as reports said the administration would likely hold some 50 Guantanamo detainees indefinitely and without charge in the United States.
The Washington Post reported that a Justice Department-led task force had recommended holding 50 of the 196 remaining men at Guantanamo without trial under the laws of war.
The men are considered too dangerous to release, but the evidence against them is insufficient to bring them to trial, according to the Post.
Though Obama outlined plans to hold some detainees without trial in a speech last year, Friday's reports were met with dismay by human rights groups who had praised his administration's pledge to close Guantanamo and uphold international law.
"One of the most shameful chapters of American history was to have been brought to a close with the shuttering of the prison at Guantanamo Bay," said Anthony Romero, executive director of the American Civil Liberties Union.
"But just as important as closing the prison quickly is closing it right and that means putting an end to the illegal policy of indefinite detention without charge or trial."
"This practice was wrong in Cuba and would remain so here, reducing the closure of Guantanamo to a symbolic gesture," he added.
The administration has indicated it plans to hold Guantanamo detainees at an Illinois prison that the federal government has acquired.
But Republican lawmakers, joined by some Democrats, fiercely oppose the prospect of bringing suspected terrorists into the United States, adding an additional obstacle to the administration's plans.
Further complicating the process is a 2008 Supreme Court decision that allows detainees to challenge their detention before US courts.
Since the decision, courts have considered a variety of cases, and overwhelmingly ruled in favor of detainees, clearing them of terrorism charges and ordering their release.
Though the administration has not set a new deadline for closing the facility, Obama's Homeland Security Secretary Janet Napolitano pledged during a visit to Spain Friday that the prison would eventually be closed.
"The goal and the intent remain the same and the will to do so is unabashed," she said.
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