There were three NORAD exercises (Sky Shield I, II, and III) in 1960, 1961, and 1962 where all civil aviation across the US and Canada were grounded for several hours (the 1961 one was 12 hours, 1960 was 6 hours and 1962 was 5.5 hours). This was with several months of advance notice. These were exercises to test how effective NORAD would be at engaging Soviet bombers. While they publicly announced that they were 99% effective, in actual fact no more than a quarter of the bombers were even engaged before they reached their target. This evaluation was not declassified until the 1990s.
After 1962 there was too much air travel to continue to shut it down for exercises, and NORAD switched to smaller, regional level things that did not shut down air travel after that. But the results of Sky Shield III in 1962 were the only experience that the FAA had to work from when they did the full ground stop after September 11th. Sky Shield III had tested how quickly air traffic control could clear the sky in the event of a nuclear war- the USAF had put up several hundred T-33 trainers, flying them randomly around the US and Canada, and then at a certain point in the exercise the ATC had to get them all on the ground far away from major metropolitan centers (presumed lost in the war).
