The architectural reconfiguration system was a component of the Doctor's TARDIS in the shape of a tree that, according to the Eleventh Doctor, "reconstruct[ed] the particles according to your needs." It was basically "a machine that makes machines". It was, according to Gregor Van Baalen's scanner, "more valuable than the total sum of any currency."
In a timeline that was later erased, Gregor stole and disconnected one of the system's orbs, and the TARDIS defended herself by locking him, Tricky and the Doctor in a continuous loop, as well as sealing the TARDIS doors. (TV: Journey to the Centre of the TARDIS)