The Supreme Court is set to hear arguments in a case challenging al-Marri's detention this April, but the Justice Department will ask the court to dismiss the case because of the indictment.
But American Civil Liberties Union attorney Jonathan Hafetz, who is representing al-Marri in the Supreme Court case challenging his detention, said yesterday that it is "vital" that the Supreme Court case move forward "because it must be made clear once and for all that indefinite military detention of persons arrested in the U.S. is illegal and that this will never happen again."
The ACLU claims that while in custody at the naval brig, the U.S. government held al-Marri incommunicado for more than a year and subjected him to torture and other abuses.
Court records filed, challenging al-Marri's custody by the military, indicate that there were videotapes of the interrogations at the brig in Charleston, S.C. The Defense Department has declined to release any tapes to al Marri's lawyers or the public.
Hafetz, who met with al-Marri Wednesday, did acknowledge yesterday that the government's decision to seek charges against al-Marri is "an important step in restoring the rule of law."
The move to charge al-Marri was widely expected in the legal community, in part because of the unique and narrow aspects of his case -- he is the only legal resident alien who is in detention in the U.S. without charges against him.
The Obama administration had asked the Supreme Court for more time to file papers in the case while it decided how it would proceed against al-Marri.
In a report in The New Yorker published earlier this week, al-Marri said through his lawyers that he is "not asking to be taken at my word and to be released, although I very much want to go home to my family."
He continued, saying that what he does want is "to be treated like every other person in the United States who is accused of a crime, including terrorism, and to be given a fair trial in an American court."
ABC News' Jan Crawford Greenburg and Ariane de Vogue contributed to this report.