Digitisation of fruit trees using LiDAR enables analysis which can be used to better growing practices to improve yield. Sophisticated analysis requires geometric and semantic understanding of the data, including the ability to discern individual trees as well as identifying leafy and structural matter. Extraction of this information should be rapid, as should data capture, so that entire orchards can be processed, but existing methods for classification and segmentation rely on high-quality data or additional data sources like cameras. We present a method for analysis of LiDAR data specifically for individual tree location, segmentation and matter classification, which can operate on low-quality data captured by handheld or mobile LiDAR. Results demonstrate viability both on real data for avocado and mango trees and virtual data with independently controlled sensor noise and tree spacing.