For most Web searching applications, queries are commonly ambiguous because words or phrases have different linguistic meanings for different Web users. The conventional keyword-based search engines cannot disambiguate queries to provide relevant results matching Web users’ intents. Traditional Word Sense Disambiguation (WSD) methods use statistic models or ontology-based knowledge systems to measure associations among words. The contexts of queries are used for disambiguation in these methods. However, due to the fact that numerous combinations of words may appear in queries and documents, it is difficult to extract concepts’ relations for all possible combinations. Moreover, queries are usually short, so contexts in queries do not always provide enough information to disambiguate queries. Therefore, the traditional WSD methods are not sufficient to provide accurate search results for ambiguous queries. In this chapter, a new model, Granular Semantic Tree (GST), is introduced for more conveniently representing associations among concepts than the traditional WSD methods. Additionally, users’ preferences are used to provide personalized search results that better adapt to users’ unique intents. Fuzzy logic is used to determine the most appropriate concepts related to queries based on contexts and users’ preferences. Finally, Web pages are analyzed by the GST model. The concepts of pages for the queries are evaluated, and the pages are re-ranked according to similarities of concepts between pages and queries.