{Here we report an adapted version of the ClearSee1 tissue clearing technique optimized for plant tissues, which enables whole plant imaging to visualize stains and expressed fluorescent proteins. This approach facilitates protein and vascular system localization in intact tissue in 3D, while retaining cellular-level structure, permitting the exploration of plant connectome interactions.Fixation and embedding of plant tissue for molecular interrogation has historically relied on techniques such as histological staining and immunohistochemistry as the foundation of plant cell biology studies, which required sectioning the tissue, labeling the section, imaging each section and then reassemble the images into a 3D representation of the structures of interest. Recent advances in fixation and tissue clearing techniques such as PEGASOS, SeeDB1, ScaleA22, iDISCO, and X-CLARITY have enabled intact imaging of animal organoids, embryos, brains and other organs. However, less attention has been given to the 3D imaging of intact plant tissues and organs. Here we present a fundamental shift from section reconstruction to tissue clearing and autofluorescence reduction, allowing for intact plant 3D visualization while retaining endogenous molecular structures of interest.}