The aim of this study is to analyse problems related to thermal mapping obtained from thermal data acquired from Unmanned Aerial Systems (UAS) equipped with thermal cameras. We focused on an accurate analysis of uncertainties introduced by the PIX4D Mapper software used to obtain the surface temperature maps of thermal images acquired by the UAS. To achieve this aim, we used artificial thermal reference during the surveys, as well as natural hot targets, i.e. thermal anomalies in the Pisciarelli hydrothermal system in Campi Flegrei caldera (CFc). Artificial thermal targets, expressly created and designed for this goal, are a prototype here called “developed thermal target” (DTT) made by the drone Laboratory at Istituto Nazionale di Geofisica e Vulcanologia - Osservatorio Vesuviano (INGV-OV). We show the results obtained by three surveys during which thermal targets were positioned on land at different flight heights of the UAS. Different heights were also necessary to test spatial resolution of the DTT with the used thermal camera as well as possible temperature differences between the raw images acquired by UAS with the thermal mapping obtained from the PIX4D Mapper software. In this work we have estimated the uncertainty that may be introduced by the mosaic procedure and furthermore we find an attenuation of the measured temperatures introduced by the different distances between the thermal anomaly and sensor. These results appear to be of great importance for the subsequent calibration phase of the thermal maps especially in cases where these methodologies are applied for monitoring purposes of volcanic/geothermal areas.