GIRI, the Grinding, Imaging and Reconstruction Instrument, was designed and built to generate 3D digital models of embedded objects in materials such as rock and metal. The instrument works by employing an automated routine of serial sectioning and imaging. Sectioning is accomplished by a precision CNC grinder. An integrated 80 megapixel camera acquires images with high precision registration and 48 bit color. This process destroys the sample while creating a permanent digital archive of serial images. Automated routines using color and textural vision algorithms isolate complex structures and objects. Hundreds of these segmented slices are combined to create 3D mathematical models. Quantities such as porosity and permeability can be computed directly from the models. Models can also be used for hydrodynamic simulation, morphological analysis, and a variety of other computational simulations. GIRI excels at identifying embedded objects with weak density contrasts that might otherwise be invisible to X-ray CT scanning methods. GIRI can process exceptionally large samples (20,000 cm3) with heterogenous characteristics.