A novel one-pass 3D thinning algorithm is proposed in this paper. 3D thinning can be regarded as an essential step in many image-processing tasks such as image quantification, image compression, motion tracking, path generation, and object navigation. The proposed algorithm generates both connected and non-connected skeletons. It is faster and more accurate than currently available techniques in the literature. In addition, it adaptively removes spurious branches of the skeleton, and hence, generates a smooth and refined skeleton, representing the essential structure of 3D elongated objects such as vessels, airways, and other similar organic shapes.