Micro-Computed Tomography (CT) is a noninvasive imaging technology that is widely used to monitor changes in lung morphology and function caused by respiratory disorders such as lung fibrosis. Here we describe the overall workflow to operate with the Quantum GX scanner in small animals to extract reliable and reproducible quantitative parameters for studying disease progression and response to treatments in the preclinical setting. To detail the post-processing procedures, we used micro-CT scans from two different mouse models of lung fibrosis, i.e., bleomycin alone or in combination with indocyanine green (ICG), which are known to be characterized by distinct radiological features.