Saqsaywaman is a UNESCO World Heritage Site in Cusco, Peru constructed by the Inca in the 15 th century. It is recognized today as a remarkable Inca engineering feat, with its most impressive features being the three Great Walls that surround it. After withstanding centuries of abuse, the structural integrity of the walls has been compromised and they are beginning to collapse. A three dimensional topographic model of Saqsaywaman revealed uncontrolled stormwater runoff to be the underlying threat to the Great Walls, resulting from the deterioration of the original Inca terracing system. Studies suggest the optimal method of protecting Saqsaywaman from further damage is to restore the Inca terracing system to its original intent to manage runoff at the site. While terrace remains are prominent on the surface of the site, the existence of a holistic terracing system at Saqsaywaman could not be justified by this alone. Thus, it was necessary to collect subsurface evidence of an Inca terracing system in addition to visual, above grade, evidence. By precisely documenting visual evidence of terraces, as well as conducting non-invasive subsurface analyses, a proposed configuration of the original terracing system was created. This terrace configuration provides a plausible recreation of the original design of Saqsaywaman supported by engineering analysis. It serves as a foundation for future studies to protect Saqsaywaman by maintaining the historical integrity at the site.