Microfocus computed tomography (micro-CT) is an imaging method that provides three dimensional (3D) digital datasets with comparable resolution to light microscopy. Although it has traditionally been used for non-destructive testing in engineering, aerospace industries and in preclinical animal studies, new applications are rapidly becoming available in the clinical setting including post-mortem fetal imaging and pathological specimen analysis. Printing three dimensional models from imaging datasets for educational purposes is well established in the medical literature, but typically using low resolution (0.7 mm voxel size) data acquired from computed tomography (CT) or magnetic resonance (MR) examinations. With higher resolution imaging (voxel sizes below 1 micron, <0.001mm) at micro-CT, smaller structures can be better characterised, and datasets post-processed to create accurate anatomical models for review and handling. In this review, we provide examples of how 3D printing of micro-CT imaged specimens can provide insight into craniofacial surgical applications, developmental cardiac anatomy, placental imaging, archaeological remains and high resolution bone imaging. We conclude with other potential future usages of this emerging technique.