In mobile device's user interface, menu organization is very important as well as menu structure because small display of mobile device. Menu items should be organized based on user knowledge structure to design user-centered interface. Traditionally, MDS (Multidimensional Scaling) have been most often used to expose users' perceived organization of menu items. But, information that MDS reveals is just relative spatial location of concepts and not relevant to concepts connection. Unlike MDS, Trajectory Mapping explicitly finds users' cognitive links between perceived concepts. This study proposes a Trajectory Mapping technique for eliciting knowledge structure, especially a set of cognitive pathways linking menu items, from end user. With twelve participants, MDS and Trajectory Mapping were conducted using cellular phone's menu items. And user knowledge structure was analyzed through Visual Concept Map that combination of results of MDS and Trajectory Mapping. After then, menu items were organized according to users' perceived organization. Empirical usability test was also conducted. The results of usability test showed that usability, in terms of task performance time, number of errors, and satisfaction, for newly organized interface was significantly improved compare to original interface. The methodology of this study is expected to be applicable to design a user-centered interface. In other words, Trajectory Mapping technique can be used as a design tool of user interface for imposing user knowledge structure on the interface.