"The most excruciating, painful things you can imagine, examples with eyes gouged. You see the pain on the face, frozen images of the last moments of life."
Among the corpses are young men - children and teenagers with ligature marks around their necks, he said.
"The regime itself has taken these photographs ... they were indexing and building files on people they'd tortured to death. They were keeping meticulous records ... the regime is so bureaucratic that it's stupid."
Rapp said it's some of the strongest evidence of state-sanctioned war crimes he's ever seen in his career.
He has no doubt that the arrest, torture and murder of thousands of Syrians over the past six years is part of a barbaric program operated by the regime itself.
"You've got facilities that are part of the regime," he said.
"They can't say this was a crazy thug doing it and they were against it ... they know. They're not doing anything about it. They're not punishing a single soul.
"We're talking about State Security, the security services here. We're talking about Military Security. Air Force Intelligence. Within the chain of command. Official forces. This is Syria."
The images and trove of documents smuggled out of the country - hundreds and thousands of pages of evidence, now kept in a secret location where investigators are building their case - are the "legal equivalent of a slam dunk", he said.
Bill Wylie, a veteran war crimes investigator, is working with Mr Rapp and says building a case against Assad will be "the final act in my career".
Among the stack of documents he's examined are internal communications, memos to the Minister of Defence and heads of intelligence and security, and damning records of imprisonment, torture and death.
"Too many people have died in detention of unnatural causes," Wylie said.
Tens of thousands of people are still missing in detention.
Those detentions began in 2011 when protests erupted throughout Syria, as the Arab Spring uprising swept across the Middle East.
Assad's forces responded with brutality, shooting people in the streets and killing scores.
It only fanned the flames of unrest, so there were orders issued to arrest people on an unprecedented scale and some 200,000 were detained in months.
One of those men was Mazen Alhummada, who told the program how he endured brutal abuse so extreme and depraved that "the human brain can't imagine it".
Officers jumped on his back until his ribs were broken, hung him by his wrists off the ground and even put a clamp on his penis.
"And he put the clamp and started tightening, squeezing, until you feel like he's going to cut off your penis," Mazen revealed. "And a man from behind puts a pole up your anus. And he is hitting you. Things that can't be imagined."
When asked how he felt about the men who'd tortured him, Mazen sat quietly sobbing for 30 seconds before responding: "God will hold them to account".
Another man detained by the Syrian regime was Ayham Halaq, a dentistry student who started working with a Syrian human rights organisation.
Their offices were raided and 13 people were detained. Ayham was beaten during interrogations but eventually released.
Six months later he was arrested against and his mother Mariam desperately searched for him without luck.
For 18 months she pleaded with government officials to tell her what happened to her son.
"They didn't tell me anything until an assistant felt sorry for me ... and (wrote a note) ... my attention immediately went to 'corpse 320'," she recalled.
The note was a summary of a file on Ayham kept by officials, stating that he died six days after he was detained.
Among the thousands of images of dead people was Ayham's.
"When I saw the photograph, I felt a great relief," Mariam said. "Now I carry it with me on my mobile phone because it's a confirmation, it's his last moments, because we didn't see his body."
While continually denying the atrocities, al-Assad labelled accusations of torture as "fake news" and propaganda designed to damage his government.
Rapp said the evidence was indisputable.
"Even the Nazis sitting in the dock at Nuremberg looking at concentration camp films were still denying it. And we don't expect confessions."
