An instructional application consists of a set of resources and activities that implement interacting, interrelated and structured experiences oriented towards achieving specific educational objectives. Computer-based instructional applications have to be looked at as any other development activity following a well defined process. With this purpose in mind, some design methods for computer-based instructional applications have been proposed. However most of them are focused on on-line courseware structures, which are quite rigid in that they have serious shortcomings in dealing with courses structured in multiple ways. Moreover, these methods usually lack a specific mechanism to model instructional concepts and strategies. This paper proposes a design framework to develop multi-structured instructional applications combining a didactic model with a software engineering approach to deal with educational and technical requirements. The underlying model extends knowledge structures, such as those involved in the Merrill's Transaction Instruction Theory, adding to them didactic information. It also considers the functional aspects of these structures. An XML-based notation is proposed to represent such structures and their management. Includes five figures. (Contains 11 references.) (Author)