Pulmonary vascular dysfunction is characterized by remodeling and loss of microvessels in the lung and is a major manifestation of chronic lung diseases (CLD). In murine models of CLD, the small arterioles and capillaries are the first and most prevalent vessels that are affected by pruning and remodeling. Thus, visualization of the pulmonary arterial vasculature in three dimensions is essential to define pruning and remodeling both temporally and spatially and its role in the pathogenesis of CLD, aging, and tissue repair. To this end, we have developed a novel method to visualize and quantitate the murine pulmonary arterial circulation using microcomputed tomography (µCT) imaging. Using this perfusion technique, we can quantitate microvessels to approximately 6 µM in diameter. We hypothesize that bleomycin‐induced injury would have a significant impact on the arterial vascular structure. As proof of principle, we demonstrated that as a result of bleomycin‐induced injury at peak fibrosis, significant alterations in arterial vessel structure were visible in the three‐dimensional models as well as quantification. Thus, we have successfully developed a perfusion methodology and complementary analysis techniques, which allows for the reconstruction, visualization, and quantitation of the mouse pulmonary arterial microvasculature in three‐dimensions. This tool will further support the examination and understanding of angiogenesis during the development of CLD as well as repair following injury.