MAV (Micro Aerial Vehicle) systems have proven useful in multiple applications (e.g. aerial photogrammetry, aerial inspections,...). For each application different sensors and even different airframes are often needed. Having a flexible UAS (Unmanned Aircraft System) devices (specifically an autopilot, a payload manager and a ground control station) that can be seamlessly used with different platforms is of great interest as it reduces the development time and effort (and hence cost). This flexibility must apply to the hardware, software and design methodologies so the system can be rapidly adapted to meet the requirements of other applications. This paper introduces a flexible system developed by CATEC consisting of an autopilot, Ground Control Station (GCS) and a payload manager for MAVs. This system has already been tested in real experiments for different applications that are also presented in this paper.