This data set provides LiDAR point clouds and digital terrain models (DTM) from surveys over the K34 tower site in the Cuieiras Biological Reserve, over forest inventory plots in the Adolpho Ducke Forest Reserve, and over sites of the Biological Dynamics of Forest Fragments Project (BDFFP) in Rio Preto da Eva municipality near Manaus, Amazonas, Brazil during June 2008. The surveys encompass the K34 eddy flux tower managed through the Large-scale Biosphere-Atmosphere Experiment in Amazonia, forest inventory plots managed by the Programa de Pesquisa em Biodiversidade (PPBio), and sites managed by the BDFFP. The LiDAR data was collected to measure forest canopy structure across Amazonian landscapes to monitor the effects of selective logging on forest biomass and carbon balance, and forest recovery over time.