The detection of archaeological heritage buried in urban areas represents today one of the most complex challenges of the cultural heritage sciences. The inter and trans disciplinary integration of archeology and geophysics can provide a significant contribution to open new perspectives and approaches addressed at improving the knowledge of the history of cities and locate the areas to be protected. The high complexity for the identification and interpretation of geophysical characteristics in the urban subsoil makes it necessary to develop ad hoc procedures to be implemented and validated in significant case studies. This work shows the results of an interdisciplinary project in Cusco (Peru), the capital of the Inca Empire, where the georadar method has been applied in urban areas of the city, in particular in courtyards of important historical palaces. This follows a published work on georadar based investigations of the main square of the city