We present in this paper the hierarchical extension of 4DReAM, a tracking framework based on a deformable model, and how we apply it in cell biology, where the use of auto fluorescent proteins and confocal microscopy enables the acquisition of the volumetric content of live cells through time sequences of 3D images (also called 4D images). Thanks to a hierarchical paradigm, 4DReAM allows interactive visualisation and analysis of the evolution of structures enclosed one in another, at different levels in the cell, such as nucleus, nucleoli, and proteins. The usefulness of our approach is illustrated on experimental results from confocal 4D images, which bring new light to the space-time reorganisation of intra-cell structures.