The use of Unmanned Aerial Systems (UASs) has increased dramatically in the recent decades. UASs are widely used for different civil applications such as land management, earth sciences, contaminant detection and monitoring and commercial use. The Autonomous Flying Platforms for Atmospheric and Earth Surface Observations project (APAESO) of the Energy, Environment and Water Research Center (EEWRC) is aimed at the dual purpose of carrying out atmospheric and earth-surface observations in the Mediterranean.The APAESO UAS platforms provide the unique ability to produce 3D measurements for determining: physical, chemical and radiative atmospheric properties, aerosol and dust concentrations and atmospheric dynamics as well as 2D investigations into: surface morphology, vegetation and land use patterns, archaeological site reconnaissance, contaminant detection and ocean surface properties (biology, waves, currents) at high spatial resolution.Through a modular design philosophy, APAESO is very adaptable for a variety of scientific investigations enabling scientific collaborations between the Cyprus Institute and national and international research organizations. Presently, the major scientific questions that can be answered using APAESO are being identified in order to determine proper design specifications and performance requirements.