The sense of presence has been the main goal of many virtual reality systems. Consequently, many research results have identified elements that contribute to high presence. However, there has been little work in applying such results to specific system and application design. In this paper, we present a model of presence that is based on the capabilities and evolutionary nature of the human perceptual system. We illustrate how we apply the model to configuring a particular virtual reality display device, the ImmersaDesk (I-desk) for a simple VR-based motion rehabilitation application. In this example, one of the important presence factors was the seamlessness and continuity (or spatial coherence) between the virtual space and the user's physical operating space. To address this problem, we present a method for correctly aligning the virtual space to the physical space.