Methods, systems, and non-transitory computer readable storage media are disclosed for reconstructing three-dimensional meshes from two-dimensional images of objects with automatic coordinate system alignment. For example, the disclosed system can generate feature vectors for a plurality of images having different views of an object. The disclosed system can process the feature vectors to generate coordinate-aligned feature vectors aligned with a coordinate system associated with an image. The disclosed system can generate a combined feature vector from the feature vectors aligned to the coordinate system. Additionally, the disclosed system can then generate a three-dimensional mesh representing the object from the combined feature vector.