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Pen-based user interfaces are becoming more popular. This paper presents the universal analysis and specification of characters and structure of pen-based user interface. With the goal of high usability, interaction techniques on pen-based user interface are performed to improve the human-computer interaction. Furthermore, based on user-centered design, This work provides a natural and harmonious pen-based user interface for collaborative design, which enhances the development and application of collaborative system. The results of the survey provide insight of pen-based user interfaces and related applications.