A method and apparatus for encoding and using user preferences in air traffic management operations are disclosed. The method may include determining a current trajectory based on the user preferences, computing a cost of deviations from the current trajectory, codifying the cost of deviations from the current trajectory using normalized cost coefficients for one or more segments of the current trajectory, and communicating the codified cost of deviations to an air traffic control (ATC) automation system, wherein the ATC automation system computes costs of maneuvers based on the codified cost of deviations and ranks the maneuvers according to cost.