The rapid evolution of 3D technology in recent years has brought about significant change in the field of agriculture, including precision livestock management. From 3D geometry information, the weight and characteristics of body parts of Korean cattle can be analyzed to improve cow growth. In this paper, a system of cameras is built to synchronously capture 3D data and then reconstruct a 3D mesh representation. In general, to reconstruct non-rigid objects, a system of cameras is synchronized and calibrated, and then the data of each camera are transformed to global coordinates. However, when reconstructing cattle in a real environment, difficulties including fences and the vibration of cameras can lead to the failure of the process of reconstruction. A new scheme is proposed that automatically removes environmental fences and noise. An optimization method is proposed that interweaves camera pose updates, and the distances between the camera pose and the initial camera position are added as part of the objective function. The difference between the camera’s point clouds to the mesh output is reduced from 7.5 mm to 5.5 mm. The experimental results showed that our scheme can automatically generate a high-quality mesh in a real environment. This scheme provides data that can be used for other research on Korean cattle.