The effects of climate change put increasing strain on rainforests and their inhabitants, highlighting the demand for technological developments to aid in biodiversity monitoring and conservation efforts. This research work proposes a novel frame work for the autonomous placement of acoustic sensor networks on top of the rainforest canopy, using a quadrotor platform. In order to tackle the challenge posed by multirotors’ limited autonomy, an initial canopy exploration mission is considered and an exploration planner is developed to detect suitable locations on top of the rainforest canopy for sensor node deployment. Specifically, green detection and pointcloud projection is performed online and combined with our proposed sampling method to accomplish targeted exploration, towards the estimated location of detected green components. Flight experiments are conducted across multiple scenarios that mimic distinct rainforest features. The results validate the system architecture and demonstrate the effectiveness of our smart sampling method, laying the foundation for future autonomous sensor network exploration missions at larger-scale.