Environmental heterogeneity occurring at small-spatial scale strongly influences the structure, composition, and functioning of tropical rainforests. Environmental filters particularly influence the establishment and survival of young individuals. The relative importance of different micro-environmental variables in shaping tree species distributions through their habitat preference and their regeneration niche however remains poorly known, due in particular to methodological limitations in the characterisation of the small-scale abiotic environment. In this study, we propose to address this knowledge gap and methodological limitation by using the latest LiDAR technology. LiDAR has already proven its ability to describe the 3D forest structure and topography on a fine scale. Forest structure and topography already allowed the prediction of important micro-climatic components for trees and notably light and associated air temperature and moisture as well as local drainage regime. LiDAR technology may also contribute to the prediction of other conditions essential to plant life: soil temperature, water and nutrient access. The LiDAR acquisition methods currently used to map forest structure have some limitations. Standard airborne laser scanning fails to describe the lower canopy in sufficient detail due to occlusion by the upper canopy. Here we explore the potential of low altitude high power laser with enhanced penetration to describe the structure of the forest understorey. We use the recorded laser pulse extinction to build a 3D model of light transmission through the canopy. We evaluate the capacity of the light transmission model to predict microclimatic variables which were monitored in the understorey for 10mo. We also derive a fine resolution digital terrain model from the airborne laser data and explore how soil characteristics covary with topographic features extracted from the DTM.