The unmanned aerial vehicle (UAV) photogrammetric survey of an archaeological site has proved itself to be particularly efficient. In order to obtain highly accurate and reliable results, it is necessary to design carefully the flight plan and the geo-referencing, while also evaluating the indicators of the accuracy rate. Using as a test case a UAV photogrammetric survey conducted on the archaeological site of the Roman Amphitheatre of Avella (Italy), in this paper, we propose a pipeline to assess the accuracy of the results according to some quality indicators. The flight configuration and the georeferencing chosen is then be checked via the residuals on the ground control points (GCPs), evenly distributed on the edges and over the entire area. With the aim of appraising the accuracy of the final model, we will suggest a method for the outlier detection, taking into account the statistical distribution (both global and of portion of the study object) of the reprojection errors. A filter to reduce the noise within the model will then be implemented through the detection of the angle formed by homologous rays, in order to reach a compromise between the number of the usable points and the reduction of the noise linked to the definition of the 3D model.