Conversion of images at micro level of normal and with very early stage disease of the lung and quantitative analysis of morphology on CT image can contribute to the chest image diagnosis to the next generation. Previous, anatomy and pathology analysis of pulmonary lobule have been conducted to better understand the CT image of peripheral lung tissue disease. However, it is difficult to figure out three-dimensional (3D) conformation because of analyzing at the slice image. The purpose of this study is a 3D microstructual and quantitative analyses of pulmonary acinus with spatial resolution in the range of several micrometers by using a synchrotron radiation micro CT (SRμCT). In this paper, we present a semi-automatic method for segmenting the secondary pulmonary lobule into acinus or subacinus and extracting small vessel in human acinus imaged by the SRμCT.