I.L.S. found on the web.

Skip all the auto pilot and look up I.L.S. (Instrument Landing System) These are autmatic now and most planes land themselves, no matter what these self professed pros here say. All someone had to do in make the aircraft I.L.S. system think that the landing strip was in actually the twin towers and that is exactly where they would go unless a human over rides it.

Here is an example of a glide scope tower, about 3 1/2 stories high that can guide an aircraft in unassisted in weather or low/no visibility conditions if 'AUTO" is selected. You could created the same glide scope anywhere on the twin towers and that is where the planes would go if the pilot was unable to over ride the auto I.L.S. system. Several firefighters that have worked airports made statements that before the second plane crash(When everyone was watching) that they saw pattern flash going up and down several out layers of the building like what you would see when guiding a plane in to an airport I.L.S. system in an emergency or vision impaired circumstance where the computer was flying the plane.
http://en.wikipedia.org/wiki/Instrument_landing_system#Use
The output from the ILS receiver goes both to the display system and can also go to a Flight Control Computer. An aircraft landing procedure can be either coupled, where the autopilot or Flight Control Computer directly flies the aircraft and the flight crew monitor the operation; or uncoupled where the flight crew fly the aircraft manually to keep the localizer and glideslope indicators centered.