The following guns were used in Aeon Flux
Shock Trooper Rifle
The Shock Trooper Rifle is a futuristic assault rifle is seen used by Shock Troopers that is a completely mocked up weapon. It has a moving 'gatling gun' style front end with multiple barrels, however all scenes of it firing are digital special effects.
Goodchild Security Rifle
A fully fabricated assault rifle is held by Goodchild security personnel. It is a lighter, single barreled sci-fi gun design and again is not based on a real firearm. Any firing sequences utilized digital special effects to simulate the gunfire in post production.
Seen used, but obscured by Sci fi outer housing, are rare FTC Airsoft Heckler & Koch P9S pistols dressed up to look like futuristic guns. Those airsoft pistols were only available for a short time between 1986-1988. One is used by Aeon Flux (Charlize Theron).
Futuristic Submachine Gun (Mocked up Glock 18)
A heavily modified Glock 18 full auto handgun is covered by a sci fi style plastic shell (to disguise the gun's origins) and was by Goodchild Guards and then by Oren Goodchild later in the movie. This was a "green gas" operated airsoft pistol, used because gas-operated airsoft handguns simulate the slide movement of the real handgun with no live firing. Like other weapons in the movie, the weapon is built on a Glock 18 (which is a real life handgun), all scenes of it firing were faked using CGI (post production digital effects). One is used by Aeon Flux (Charlize Theron).