Digital Elevation Models (DEMs) are 3D representations of the Earth’s surface and have numerous applications in geomorphology, hydrology and ecology. Structure-from-Motion (SfM) photogrammetry using photographs obtained by unmanned aerial vehicles (UAVs) have been increasingly used for obtaining high resolution DEMs. These DEMs are interpolated from point clouds representing entire landscapes, including points of terrain, vegetation and infrastructure. Up to date, there has not been any study clearly comparing different algorithms for filtering of vegetation. The objective in this study was, therefore, to assess the performance of various vegetation filter algorithms for SfM-obtained point clouds. The comparison was done for a Mediterranean area in Murcia, Spain with heterogeneous vegetation cover. The filter methods that were compared were: color-based filtering using an excessive greenness vegetation index (VI), Triangulated Irregular Networks (TIN) densification from LAStools, the standard method in Agisoft Photoscan (PS), iterative surface lowering (ISL), and a combination of iterative surface lowering and the VI method (ISL_VI). Results showed that for bare areas there was little to no difference between the filtering methods, which is to be expected because there is little to no vegetation present to filter. For areas with shrubs and trees, the ISL_VI and TIN method performed best. These results show that different filtering techniques have various degrees of success in different use cases. A default filter in commercial software such as Photoscan may not always be the best way to remove unwanted vegetation from a point cloud, but instead alternative methods such as a TIN densification algorithm should be used to obtain a vegetation-less Digital Terrain Model (DTM).