Nowadays biomedical engineers regularly have to combine data from multiple medical imaging modalities, biomedical measurements and computer simulations and this can demand the knowledge of many specialised software tools. Acquiring this knowledge to the depth necessary to perform the various tasks can require considerable time and thus divert the researcher from addressing the actual biomedical problems. The aim of the present study is to describe a new application called the Multimod Data Manager, distributed as a freeware, which provides the end user with a fully integrated environment for the fusion and manipulation of all biomedical data. The Multimod Data Manager is generated using a software application framework, called the Multimod Application Framework, which is specifically designed to support the rapid development of computer aided medicine applications. To understand the general logic of the Data Manager, we first introduce the framework from which it is derived. We then illustrate its use by an example—the development of a complete subject-specific musculo-skeletal model of the lower limb from the Visible Human medical imaging data to be used for predicting the stresses in the skeleton during gait. While the Data Manager is clearly still only at the prototype stage, we believe that it is already capable of being used to solve a large number of problems common to many biomedical engineering activities.