A Web site is a hyperlinked network environment, which consists of hundreds of inter-connected pages, usually without an engineered architecture. This is often a large, complex Web site that is difficult to understand and maintain. In this paper, we propose an approach that aims to restructure an existing Web site by adapting them to a controller-centric architecture. In particular, this approach is twofold. First, it defines a domain model to represent dependencies between Web pages in order to abstract current structure of the Web site. Second, it designs a system architecture as a reference model for restructuring the Web site to the new structure. These principles will be illustrated through a case study using a reengineering tool that implements the refactoring process for a JSP-based Web site.