The alveolated structure of the pulmonary acinus plays a vital role in gas exchange function. Three-dimensional (3D) analysis of the parenchymal region is fundamental to understanding this structure-function relationship, but only a limited number of attempts have been conducted in the past because of technical limitations. In this study, we developed new image processing methodology based on Finite Element analysis for accurate 3D structural reconstruction of the gas exchange regions of the lung. Stereologically well characterized rat lung samples (Pediatr. Res. 53:72-80. 2003) were imaged using high resolution synchrotron radiation based x-ray tomographic microscopy. A stack of 1024 images (each slice: 1024x1024 pixels) with resolution of 1.4³ µm³ per voxel were generated. For the development of FE algorithm, regions of interest (ROI), containing approximately 7.5 million voxels, were further extracted as a working subunit. 3D Finite-Elements were created overlaying the voxel map using a grid-based hexahedral algorithm (GBHA). A proper threshold value for appropriate segmentation was iteratively determined to match the calculated volume density of tissue (V_Vs) to the stereologically determined value (Pediatr. Res. 53:72-80. 2003). The resulting 3D Finite Elements are ready to be used for 3D structural analysis as well as for subsequent FE computational analyses like Fluid Dynamics and Skeletonization.