Resumen: Alveolar architecture plays a fundamental role in the processes of ventilation and perfusion in the lung. Alterations in the alveolar surface area and alveolar cavity volume constitute the pathophysiological basis of chronic respiratory diseases such as pulmonary emphysema. Previous studies based on micro-computed tomography (micro-CT) of lung samples have allowed the geometrical study of acinar units. However, our current knowledge is based on the study of a few tissue samples in random locations of the lung that do not give an account of the spatial distributions of the alveolar architecture in the whole lung. In this work, we combine micro-CT imaging and computational geometry algorithms to study the regional distribution of key morphological parameters throughout the whole lung. To this end, 3D whole-lung images of Sprague–Dawley rats are acquired using high-resolution micro-CT imaging and analyzed to estimate porosity, alveolar surface density, and surface-to-volume ratio. We assess the effect of current gold-standard dehydration methods in the preparation of lung samples and propose a fixation protocol that includes the application of a methanol-PBS solution before dehydration. Our results show that regional porosity, alveolar surface density, and surface-to-volume ratio have a uniform distribution in normal lungs, which do not seem to be affected by gravitational effects. We further show that sample fixation based on ethanol baths for dehydration introduces shrinking and affects the acinar architecture in the subpleural regions. In contrast, preparations based on the proposed dehydration protocol effectively preserve the alveolar morphology.