A dispatcher at the airline is assigned to the flight and starts with the “usual” route it flies that minimizes fuel use and is usually the shortest path. Then they look at weather along the route that day, upper wind forecasts, and traffic flow programs that in the U.S. anyway the central ATC headquarters communicates to all the major airlines throughout the day. The dispatcher then “files” their requested route with ATC. About a half hour before departure, ATC confirms the routing (or might make minor changes if situations have changed) and the pilots get an automated printout or verbal confirmation of their route.
They then program it into their onboard navigation system. After departure, ATC occasionally may have a re-route mostly due to weather or traffic flow, or often the pilots will request shortcuts if they are running late.
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