Criticism comes from some lawmakers and some of the families of Americans killed in the attacks.
Memories of their son, Dan Shanower, occupy a corner of the living room in his parents' Naperville home and a big part of their thoughts every day.
Shanower, a Naval intelligence officer, was killed in the Pentagon on 9/11.
Don and Pat Shanower say they are glad those who allegedly plotted the attacks may finally go on trial soon in this country.
"In America, you get a fair trial and a just trial," said Don Shanower.
"We have to give the same rights to the despicable ones as you would like for yourself if you were accused of something," said Pat Shanower.
It will also likely be the biggest trial since the Nazi war crime trials in Nuremburg after World War II.
"I am absolutely convinced that Khalid Sheikh Mohammed will be subject to the most exacting demands of justice. The American people will insist on it and my administration will insist on it," President Barack Obama said.
Some New Yorkers who lost loved ones to the terrorism of 9/11 are critical of the decision.
"New York City is still recovering from 9/11 and to have it come back here and to have the scar ripped open again, for me, I think that's going to be a tremendous hardship," said Lee Lelpi Father of 9/11 Victim
"I am absolutely outraged. This is the most disgraceful decision any president has ever made," said Rep. Peter King, (R) New York.
Investigators may use video of Osama bin Laden bragging about the massacre.
But some question the strength of government's case without the use of confessions that were gathered through torture and would likely be inadmissible in court.
But the attorney general says he's confident in the case. And he will ask for the ultimate penalty.
"these were extraordinary crimes. I fully expect to direct prosecutors to seek the death penalty," said Eric Holder, U.S. attorney general.At a news conference, the attorney general said five other suspects, including a major suspect in the bombing of the USS Cole, Abd al-Rahim al-Nashiri, will be tried before a military commission.
Holder said the detainees in the New York case will be tried in a courthouse just blocks from where the Sept. 11 attackers felled the twin towers. Bringing such notorious suspects to U.S. soil to face trial is a key step in President Barack Obama's plan to close the terror suspect detention center at Guantanamo Bay, Cuba. Obama initially planned to close the detention center by Jan. 22, but the administration is no longer expected to meet that deadline.
"For over 200 years our nation has relied upon a faithful adherence to the rule of law," Holder told a news conference at the Justice Department. "Once again, we will ask our legal system in two venues to answer that call."
The plan that Holder outlined Friday is a major legal and political test of Obama's overall approach to terrorism. If the case suffers legal setbacks, the administration will face second-guessing from those who never wanted it in a civilian courtroom. And if lawmakers get upset about terrorists being brought to their home regions, they may fight back against other parts of Obama's agenda.
"This is definitely a seismic shift in how we're approaching the war on al-Qaida," said Glenn Sulmasy, a law professor at the U.S. Coast Guard Academy who has written a book on national security justice. "It's certainly surprising that the five masterminds, if you will, of the attacks on the United States will be tried in traditional, open federal courts."
The New York case may force the court system to confront a host of difficult legal issues surrounding counterterrorism programs begun after the 2001 attacks, including the harsh interrogation techniques once used on some of the suspects while in CIA custody. The most severe method -- waterboarding, or simulated drowning -- was used on Mohammed 183 times in 2003, before the practice was banned.
The Associated Press contributed to this report.