The structure of a Web site can prevent the search robots or crawling agents from confusion in the midst of huge forest of the Web pages. We formalize the view on the World Wide Web and generalize it as a hierarchy of Web objects such as the Web as a set of Web sites, and a Web site as a directed graph with Web nodes and Web edges. Our approach results in the optimal hierarchical structure that can maximize the weight, tf-idf (term frequency and inverse document frequency), that is one of the most widely accepted content centric measures in the information retrieval community, so that the measure can be used to embody the semantics of search query. The experimental results represent that the optimization model is an effective alternative in the dynamically changing Web environment by replacing conventional heuristic approaches.