A system and a method for generating a 3D path from a source to a destination for an aerial vehicle is disclosed. An example system includes a managing unit to select a group of altitude layers including source and destination and generate a 2D horizontal scenario by identifying constraints to avoid at each altitude layer. The example system includes a path computing unit to determine common constraints for the altitude layers of the 2D horizontal scenario and compute a 2D lateral path avoiding the common constraints. The managing unit generates a 2D vertical scenario based on a projection of the previously computed 2D lateral path onto the constraints at the altitude layers. The path computing unit computes a 2D vertical path avoiding constraints of the 2D vertical scenario. The managing unit composes 3D waypoints of a conflict-free 3D path according to the 2D lateral path and 2D vertical path.