Context. In the forthcoming years Healthcare Systems will become better informed, more efficient and particularly focused on the patient through the integration of Information and Communication Technologies. Medical Rehabilitation is an example of a field prone for this evolution. Here, disciplines such as Software Engineering will play a key role during the transformation. Objectives. This study pursues to understand todays rehabilitation therapies and procedures, to conceive how future computer-aided rehabilitation systems should be constructed and to provide a coherent framework that conceptualizes the relationship of their main components and interactions. Methods. The overall thesis work involves a combination of different research methodologies, which vary from literature reviews, empirical observations and semi-structured ethnographic interviews, to constructive research, through software architectural designs. Results. FIAP-RT is a framework created to support the new paradigm on how future software tools oriented to Medical Rehabilitation should be constructed with views to achieve quality attributes such as interoperability, availability, security, accessibility, usability or reliability. Conclusions. This study reveals that it is generally hard to find a real socialization and dissemination of the know-how that is being constantly produced within rehabilitation centers. In addition, it is has been shown how applied Software Engineering can help to integrate advanced solutions even though further evaluation would be needed to validate the proposed framework.