We report the results of drone lidar survey at a high-elevation archaeological site in the Chachapoyas region of Peruvian Amazonia. Unlike traditional airborne remote sensing, drone lidar produces very high-density measurements at a wide range of scan angles by operating at low altitudes and slow flight speeds. These measurements can resolve near vertical surfaces and novel dimensions of variability in architectural datasets. We show in a case study at Kuelap that the number of detected structures almost exactly matches the number reported from previous ground level surveys, and we use these data to quantify the relative circularity and size frequency distribution of architectural structures. We demonstrate variability in domestic architecture that was obscured in previous models produced using low-resolution remote sensing. Spatial analysis of these attributes produces new hypotheses about the site’s construction history and social organization.