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By NBC News

BAGHDAD — The primitive cages look like they once housed dangerous animals.

Cramped and dilapidated, the seven miniature prisons stand in a room marked by peeling paint and smashed floor tiles deep in the Iraqi city of Fallujah.

Keeping animals in these enclosures would be cruel. But as recently as June, they held humans — ISIS prisoners, many of whom were about to be executed.

Cages that ISIS used to hold prisoners in Fallujah.NBC News

"They used to imprison locals in iron cages like animals," Iraqi Army Brig. Jalil Abdulredha told NBC News just outside the room. "They made different shapes of cages for different positions, such as kneeling and standing. This shows the brutality of this terrorist organization."

ISIS controlled Fallujah between January 2014 and June, when Iraqi troops backed by U.S.-led airstrikes liberated the city — which is located just 30 miles from Baghdad.

While ISIS was driven out of Fallujah, remnants of their presence remain.

One is the prison and makeshift cells that NBC News saw during a visit with the military last week.

Another vestige of ISIS' rule is next door to the prison — a crude courthouse where the extremists upheld their version of law and order.

Security forces gather outside ISIS' main courthouse in Fallujah.NBC News

The building, which served as ISIS' main "court" in Fallujah, features surprisingly untarnished art deco ceiling, complete with chandelier and geometric moulding. However, these decorative flourishes fade away into blackened wallpaper and muddy tiles.

A cleaner patch of wall behind the judge’s bench appears to have once housed a banner. In its place hangs the unmistakable black-and-white flag of ISIS.

Scruffy wooden chairs and desks dot the room, mimicking the layout of many small courthouses in the U.S. The justice meted out here, however, was anything but familiar.

"Most of [the defendants] were innocent locals and members of security forces," according to Abdulredha.

Inside ISIS' main courthouse in Fallujah.NBC News

He said people were found guilty for refusing to join ISIS' ranks — or they faced punishments for violating the group's ultra-conservative interpretation of Islamic law, known as Shariah.

When troops stormed the building, they found documents containing names of some of those tried and killed at the courthouse, Abdulredha said. But none of the officials contacted by NBC News — including the U.S. military, the United Nations and the Iraqi government — were able to put an estimate on the number of lives lost there.

"ISIS have created their own rules and laws according to what they think is taken from the Islamic law," Abdulredha said. "In fact, they are far away from being Muslims."

Before ISIS took control, these buildings were upmarket houses.

In another neighborhood of Fallujah around a mile away, Iraqi troops found an improvised graveyard where around 300 ISIS fighters were buried. The cemetery was little more than a collection of tiles and paving stones lying on mounds of earth, with the names of those entombed written in blue pen alongside the date of their death.

Iraqi soldiers check an ISIS cemetery on Sept. 4.AHMAD AL-RUBAYE / AFP - Getty Images

"Behind me is the graveyard of the terrorists of ISIS," said Brig. Yahya Rasool, a spokesman of the Joint Operation Command formed by U.S. and Iraqi forces. "They are from Arab and eastern Asia countries. They have been killed before and during the fighting to liberate Fallujah. Many of them are well-known."

Now, security forces are working to clear the city of bombs and booby-traps before its population — tens of thousands of whom fled the violence — can start to think about moving back in.

"A military engineering team will have to be sure that houses are cleared before the return of any family to their house," Rasool said.

About 10 percent of Fallujah has been destroyed, he added. The city and provincial councils will now work with the national government to rebuild and provide people with public services.

The aim, he said, is "to have Fallujah completely ready for the return of its people."

Alexander Smith contributed.