In Fukushima and the surrounding area, decontamination work is performed by removing radioactive materials, mainly containing radioactive cesium, from soil surfaces, grass and trees, and buildings. The decontamination waste is put in container bags and brought to temporary storage sites. To prevent infiltration of rainwater into the stored waste, bags must be capped with impervious geomembrane sheets or air-permeable waterproof sheets. Visual inspection is normally used to determine the soundness of such liners. However, the area of the storage site is very large and there are more than 1000 storage sites constructed by the government and municipal administrations. It is difficult to cover entire storage sites with the limited information from visual inspection by workers. Aerial monitoring with drones is one effective method to help solve such problems. A questionnaire revealed that the most common cause of damage to upper capping liners was stress from rainwater puddles on the capping. 3D models could be used for deformation evaluation of capping liners and estimating volumes of puddles. This study generated 3D models via SfM analysis of the images photographed by drones and aimed to develop a method to estimate the damage endangered area by estimating the tensile stress and strain distribution with FEM using the coordinate data of the point groups forming the 3D models as the input data.