MOTIVATION: Developing methods to efficiently analyze 3D point cloud data of plant architectures remain challenging for many phenotyping applications. Here, we describe a tool that tackles four core phenotyping tasks: classification of cloud points into stem and lamina points, graph skeletonization of the stem points, segmentation of individual lamina and whole leaf labeling. These four tasks are critical for numerous downstream phenotyping goals, such as quantifying plant biomass, performing morphological analyses of plant shapes and uncovering genotype to phenotype relationships. The Plant 3D tool provides an intuitive graphical user interface, a fast 3D rendering engine for visualizing plants with millions of cloud points, and several graph-theoretic and machine-learning algorithms for 3D architecture analyses. AVAILABILITY AND IMPLEMENTATION: P3D is open-source and implemented in C++. Source code and Windows installer are freely available at https://github.com/iziamtso/P3D/. CONTACT: [email protected] or [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.