Reducing the impact on the environment and the associated commercial implications are two major challenges that the global commercial aviation industry is addressing with significant commitment today. In this respect, Clean Sky, which is a 1.6 billion Joint Technology Initiative part funded by the European Commission is the largest ever programme addressing the greening of air transportation in response to the Advisory Council for Aeronautics Research in Europe (ACARE) goals of reducing CO2 and perceived noise emissions by 50% and NOx by 80% by 2020 compared to 2000 condition. This paper presents research work carried out within the Systems for Green Operations Integrated Technology Demonstrator (ITD) of Clean Sky that is associated with GATAC, a trajectory and route planning tool to enable the multi-objective optimization of flight trajectories and missions. The design and operational methodology of the tool, the optimization algorithms and models are discussed and the results of a preliminary application for a long-range commercial flight are presented.