In various engineering applications, remote sensing images such as digital elevation models (DEMs) and orthomosaics provide a convenient means of generating 3D representations of physical assets, enabling the discovery of new insights and analyses. However, the presence of noise and artefacts, particularly unwanted natural features, poses significant challenges, and their removal requires the application of filtering techniques prior to conducting analysis. Unmanned aerial vehicle-based photogrammetry is used at Melbourne Water’s Western Treatment Plant as a cost-effective and efficient method of inspecting the floating covers on the anaerobic lagoons. The focus of interest is the elevation profile of the floating covers for these sewage-processing lagoons and its implications for sub-surface scum accumulation, which can compromise the structural integrity of the engineered assets. However, unwanted artefacts due to trapped rainwater, debris, dirt, and other irrelevant structures can significantly distort the elevation profile. In this study, a machine learning algorithm is utilised to group distinct features on the floating cover based on an image segmentation process. An unsupervised k-means clustering algorithm is employed, which operates on a stacked 4D array composed of the elevation of the DEM and the RGB channels of the associated orthomosaic. In the cluster validation process, seven cluster groups were considered optimal based on the Calinski–Harabasz criterion. Furthermore, by utilising the k-means method as a filtering technique, three clusters contain features related to the elevations associated with the floating cover membrane, collectively representing 84% of the asset, with each cluster contributing at least 19% of the asset. The artefact groups constitute less than 6% of the asset and exhibit significantly different features, colour characteristics, and statistical measurements from those of the membrane groups. The study found notable improvements using the k-means filtering method, including a 59.4% average reduction in outliers and a 36.3% decrease in standard deviation compared to raw data. Additionally, employing the proposed method in the scum hardness analysis improved correlation strength by 13.1%, removing approximately 16% of the artefacts in total assets, in contrast to a 3.6% improvement with the median filtering method. This improved imaging will lead to significant benefits when integrating imagery into deep learning models for structural health monitoring and asset performance.