The Hijackers turned off the aircraft's IFF transponders. Most large-area radars operate secondary only, so would have disappeared from alot of ATC radar screens, making them difficult to track. Primary radar would still have picked them up, but they would have been one (unlabelled) dot among many hundreds. I believe their flightpaths have been reconstructed post-facto from ATC tapes.
How's that for a kick-off?
16B