In 2006 and 2008 the Bureau of Prisons quietly opened self-contained isolation units at Terre Haute, Indiana and Marion, Illinois — Communication Management Units, where prisoners' calls, visits, and letters are drastically restricted, monitored live, and barred from all physical contact with family, some seeing children only through glass for years. Created without the legally required public rulemaking, the units held populations that were roughly two-thirds Muslim — the war on terror's defendants — leavened with political cases: Daniel McGowan of Operation Backfire and animal-rights organizer Andrew Stepanian both did time there, and prisoners called the units "Little Guantánamo."

Documents produced in the Center for Constitutional Rights' lawsuit Aref v. Lynch showed prisoners designated for the units on the basis of their "anti-government" and "extremist" beliefs, protected speech in prison newsletters among the cited grounds; McGowan was returned to a CMU after publishing an article about the units themselves. The litigation won procedural review but left the units standing — a permanent architecture, born in the Green Scare years, for segregating prisoners by ideology and severing them from the movements that support them.