Detailed descriptions of 3-D anatomically preserved specimens in paleobotany have been undertaken for over 100 years. Some of the most comprehensively characterised of these specimens are reproductive structures, especially cones and ovules. Throughout this time many of the ways of gaining information such specimens has remained static. In recent years new computer software and techniques have been developed that allow detailed 3- D computer reconstructions to be undertaken that allow holistic observations of the context of the whole organ. Detailed 3-D reconstructions have been undertaken of several genera of Palaeozoic and Mesozoic paleobotanical reproductive organs. These complex structures have undergone traditional preparation, such as serial sectioning, preparation specifically for reconstruction such as serial grinding and non-destructive scanning micro X-ray tomography. Reconstructions were then produced in bespoke software, Serial Paleontological Image Editing and Rendering System (SPIERS). The reconstructions produced provide a new understanding to the structure and functions of tissues within paleobotanical reproductive specimens. For the first time, specimens of extinct and extant genera have been compared using new reconstruction techniques in order to aid in the future understanding of their evolution and development, and to aid visualisation of complex structures for which illustrations in 2-D form are inadequate.