This paper presents an autonomous approach to tree detection and segmentation in high resolution airborne LiDAR that utilises state-of-the-art region-based CNN and 3D-CNN deep learning algorithms. If the number of training examples for a site is low, it is shown to be beneficial to transfer a segmentation network learnt from a different site with more training data and fine-tune it. The algorithm was validated using airborne laser scanning over two different commercial pine plantations. The results show that the proposed approach performs favourably in comparison to other methods for tree detection and segmentation.