To combine the affordances of paper and computers, prior research has proposed numerous interactive paper systems that link specific paper document content to digital operations such as multimedia playback and proofreading. Yet, it remains unclear to what degree these systems bridge the inherent gap between paper and computers when compared to existing paper-only and computer-only interfaces. In particular, given the special properties of paper, such as limited dynamic feedback, how well does an average new user learn to master the interactive paper system? What factors affect the user performance? And how does the paper interface work in a typical use scenario? To answer these questions, we conducted two empirical experiments on a generic pen gesture based command system, called PapierCraft [Liao, et al., 2008], for paper-based interfaces. With it, people can select sections of printed document and issue commands such as copy and paste, linking and in-text search. The first experiment focused on the user performance of drawing pen gestures on paper. It proves that users can learn the command system in about 30 minutes and achieve a performance comparable to a Table PC-based interface supporting the same gestures. The second experiment examined the application of the command system in Active Reading tasks. The results show promise for seamless integration of paper and computers in Active Reading for their combined affordances. In addition, our study identifies some key design issues, such as the pen form factor and feedback of gestures. This paper contributes to better understanding on pros and cons of paper and computers, and sheds light on the design of future interfaces for document interaction.