In higher-plant cells, microtubules, actin microfilaments, and vacuoles play important roles in a variety of cellular events, including cell division, morphogenesis, and cell differentiation. These intracellular structures undergo dynamic changes in their shapes and functions during cell division and differentiation, and to analyse these sequential structural changes, the vital labelling technique, using the green-fluorescent protein or other fluorescent proteins, has commonly been used to follow the localisation and translocation of specific proteins. To visualise microtubules, actin filaments, and vacuoles, several strategies are available for selecting the appropriate fluorescent-protein fusion partner: microtubule-binding proteins, tubulin, and plus-end-tracking proteins are most suitable for microtubule labelling; the actin binding domain of mouse talin and plant fimbrin for actin microfilament visualisation; and the tonoplast-intrinsic proteins and syntaxin-related proteins for vacuolar imaging. In addition, three-dimensional reconstruction methods are indispensable for localising the widely distributed organelles within the cell. The maximum intensity projection method is suitable for cytoskeletal structures, while contour-based surface modelling possesses many advantages for vacuolar membranes. In this article, we summarise the recent progress in living cell imaging of the plant cytoskeleton and vacuoles using various fusions with green-fluorescent proteins and three-dimensional imaging techniques.