In a pen-based computing system, use of paradigms similar to those used with physical paper to organize user generated content captured by a smart pen is disclosed. Data, such as handwriting gestures, is captured by the smart pen and transferred to a digital domain, such as by being transferred to a computing system. Once in the digital domain, the captured content is organized as virtual pages or virtual notebooks. Hence, content captured from various sources, such as different notebooks or different physical pieces of paper, is assembled into a virtual page or virtual notebook. User input or automatic application of rules can be used to assemble the captured content into a virtual page or virtual notebook.