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Recent advances in the research of autonomous vehicles have showed a vast range of applications, such as exploration, surveillance and environmental monitoring. Considering the mining industry, it is possible to use such vehicles in the prospection of minerals of commercial interest beneath the ground. However, tasks such as geophysical surveys are highly dependent on specific sensors, which mostly are not designed to be used in these new range of autonomous vehicles. In this work, we propose a novel magnetic survey pipeline that aims to increase versatility, speed and robustness by using autonomous rotary-wing Unmanned Aerial Vehicles (UAVs). We also discuss the development of a state-of-the-art three-axis fluxgate, where our goal in this work was to refine and adjust the sensor topology and coupled electronics specifically for this type of vehicle and application. The sensor was built with two ring-cores using a specially developed stress-annealed CoFeSiB amorphous ribbon, in order to get sufficient resolution to detect concentrations of small ferrous minerals. Finally, we report on the results of experiments performed with a real UAV in an outdoor environment, showing the efficacy of the methodology in detecting an artificial ferrous anomaly.