The Federal Aviation Administration (FAA) is one of the largest Air Navigation Service Providers, managing air traffic for more than 15% of the world’s airspace. Today’s Air Traffic Control (ATC) system cannot meet the growth of the air traffic activities, which brings with more unprecedented delays. At the same time, Air Traffic Controllers are facing higher workload than ever before. The FAA has declared that the existing ATC system will transition to a new system known as “Free Flight”. “Free Flight” will change today’s ATC system by giving pilots increased flexibility to choose and modify their routes in real time, thereby reducing cost and increasing system capacity. In this work, the modules and data flow of the next generation ATC system is designed, and their Petri net models are constructed for the control module to achieve “Free Flight”.