Soufan argues that terrorists like Abu Zubaydah have been trained to expect extremely brutal treatment in Middle Eastern prisons, which is one reason he believes enhanced interrogation techniques are not effective.
"If you look at them from an American perspective, you will say, 'Wow, that's torture.' But really that's like saying hello in some jail in the Middle East," Soufan said.
"This is not the torture that these guys are expecting," he continued. "So why do we start going on a path that eventually we're gonna hit a glass ceiling? And when you hit the glass ceiling, what do you do? "
"What do you do?" Logan asked.
"The detainee calls your bluff. You cannot go back and say, 'I'm gonna build a rapport.' That's why you keep repeating the glass ceiling again and again and again and again. Abu Zubaydah was waterboarded 83 times, Khalid Sheikh Mohammed 183 times. What does that tell you? Does that tell you the technique is working?"
A number of people in the CIA and the intelligence community told us that Abu Zubaydah did give up information after he was waterboarded, which they say helped save American lives and that, all moral questions aside, the enhanced interrogation program yielded significant intelligence; including information that contributed to the killing of Osama bin Laden.
"At least two former directors of the CIA, George Tenent and Michael Hayden say that enhanced interrogation techniques do work," Logan said.
"Sure, sure," Soufan said.
"They have access to more intelligence than you," Logan said.
"Absolutely," Soufan replied.
"If you don't know everything, how can you be so sure that they don't work?" Logan asked.
"Because I am privy to a lot of information that also I'm not telling you here," Soufan said.
"But is it possible for you to know all the information, everything that may or may not have been gained from these techniques?" Logan asked.
"I'm not claiming that I know everything. I know what I know," Soufan replied.
The one thing that has caused Ali Soufan more anguish than anything else is the thought that the events of 9/11 might have been prevented if, he says, the CIA had shared certain information with him and his FBI team.
While they were investigating the attack on the USS Cole in November 2000, Soufan's team learned that an al Qaeda operative had met with other terrorists in Asia and received a large sum of money. Soufan says he made three formal requests through the FBI to the CIA to see if anything was known about what this operative was up to. Each time, he says, the CIA indicated that it did not know anything.
But, Soufan says he later learned the CIA knew - eight months before 9/11 - that this same operative had met in Malaysia with two terrorism suspects who would later hijack the plane that crashed into the Pentagon. And the CIA also knew that those two suspects were heading to the U.S.
"The agency knew that these al Qaeda operatives in Southeast Asia flew to America or they have visas to come to the United States, and somebody decided, 'Let's not share the information,'" Soufan said.
"And if it had been shared with you, what then?" Logan asked.
"I try not to think about that. I try not to think about, about what could have happened. Maybe, maybe thousands of American lives will be spared, maybe," Soufan said.
The CIA told us any suggestion it purposely refused to share critical information on the 9/11 plots with FBI is "baseless" and "these allegations diminish the hard work and dedication of countless CIA officers."