When a military judge threw out a defendant's confession in the Sept. 11 case this month, he gave two main reasons. The prisoner's statements, the judge ruled, were obtained through the C.I.A.'s use of torture, including beatings and sleep deprivation. But equally troubling to the judge was what happened to the prisoner in the years after his physical torture ended, when the agency held him in isolation and kept questioning him from 2003 to 2006. The defendant, Ammar al-Baluchi, is accused of sending money and providing other support to some of the hijackers who carried out the terrorist attack, which killed 3,000 people. In court, Mr. Baluchi is charged as Ali Abdul Aziz Ali. He is the nephew of Khalid Shaikh Mohammed, the man accused of masterminding the plot. The judge, Col. Matthew N. McCall, wrote that it was easy to focus on the torture because it was "so absurdly far outside the norms of what is expected of U.S. custody preceding law enforcement questioning." "However," he added, "the three and a half years of uncharged, incommunicado detention and essentially solitary confinement all while being continually questioned and conditioned " is just as egregious" as the physical torture. Prosecutors are preparing to appeal. But the 111-page ruling was the latest blow to the government's two-decade-old effort to hold death penalty trials at Guantánamo Bay by sweeping aside a legacy of state-sponsored torture.