The problem of geological studies carried out in prospective areas characterized by complex landscape-morphological conditions and their remoteness from infrastructure has been analyzed. The paper provides an overview of available approaches to conducting magnetic surveys, a universal method applicable for geological mapping and prospecting that proved very efficient in various geologic settings. The main technical features of a hardware and software system developed by the authors for unmanned low-altitude aeromagnetic surveys are described. This aeromagnetic system is meant to operate in difficult environment conditions. Some actual problems of developing airborne geophysical systems are considered and their solutions proposed by the authors are introduced. Due to original techniques and procedures the designed aeromagnetic complex provides large scale data, which is achieved due to the low cost of the used components and their high reliability, as well as a possibility for making taking measurements at extremely low altitudes with a relief flow even in mountainous areas. For this purpose, the authors have developed a geoinformation module named a SibGIS Flight Planner which provides an automated preparation of flight missions taking into account accurate information about a terrain model and its uploading in a data format supported by common autopilot systems. Like the rest of the complex software modules, this plugin is designed for freeware GIS QuantumGIS. It provides a true layout of networks with profiles and measurement stakes, determination of flight altitudes for mission points, setting a large number of flight parameters and uploading resulting files in the *.awm format. Since this software can be used in a wide range of tasks related to professional use of unmanned aerial vehicles (UAVs), the authors consider it possible to open the source code of the module (https://github.com/raulett/SibGIS-Flight-Planner), as well as provide a link to download the finished plug-in, which now can be used by any interested specialist. We also give some internet links to field exploration videos demonstrating the UAV complex abilities mentioned in the article, in particular a flight at extremely low altitudes around the terrain relief, and activities in difficult weather conditions and at low temperatures.Keywords: UAV, aerogeophysics, magnetic survey, geoinformation systems.