In this paper, the initial work of realizing a robust unmanned aerial remote sensing system, equipped with a survey-grade Lidar scanner and a multispectral camera, to study the pre-Columbian Amazonian archaeology are presented. The data collected from this system will be utilized in a novel inter-disciplinary way by combining these data with in-situ data collected by archaeologists, geographers and other specialists to study the nature and scale of the impact of pre-Columbian humans in transforming the landscapes of the Amazonian rainforest. The outputs of this project will also give us insight on the conservation and sustainability of the forest.