Two-dimensional micro-computed tomography (micro-CT) slices can be reconstructed into three-dimensional (3D) models that demonstrate capillary beds. This study focused on the acquisition of data necessary to create scaffolding that directly mimics the unique structural patterns of a microvascular tree system. The Microfil vascular contrasting method was compared to the Baston's methylmethacrylate corrosion casting (BMCC) method to determine which provided the most accurate and high-resolution results for 3D micro-CT reconstruction derived from the two-dimensional micro-CT slices of the capillary beds. It was determined that the BMCC, a method traditionally used in the scanning electron microscopic analysis of the microvasculature, was the best method for representing capillary lumina for micro-CT scanning. The removal of tissues from the BMCC cast resulted in samples that eliminated background material, thus increasing the X-ray contrast levels of the CT images. This provided for a more complete and more distinguishable high-resolution image of the represented capillary lumina. Images created with this BMCC method were reconstructed in a stereolithography file format as 3D mesh structure for later importing into computer-aided design (CAD) software. The resulting Bio-CAD, then, can be used to guide the more accurate fabrication of the microvascular scaffolding and then serve as the framework for tissue engineering of microvascular structures. Results from this study clearly indicated that the BMCC method is superior to the Microfil method for accurate and complete high-resolution imaging of capillary beds.