(Speaking hypothetically in the case of WTC and the Pentagon - )
There are a couple of "remote control" methodologies - the most primitive being the one used by RC modelers 50+ years ago. The "pilot" had to have eye contact with the RC plane and its environment, and operated the controls surface(s) directly through his transmitter.
Add a forward viewing video camera and you can aim it pretty effectively - remote controlled bombs work like this. There's good bombs-eye video of a RR bridge in Yugoslavia being hit with one.
Stability augmentation - steering via autopilot - makes it easier to control.
Finally, you can have an autonomous UAV like Global Hawk - you program it with an objective, and a base for recovery, and away it goes on its own.
But there's no good evidence any of this applied on 9/11.