Paper persists as an integral component of active reading and other knowledge-worker tasks because it provides ease of use unmatched by digital alternatives. Paper documents are light to carry, easy to annotate, rapid to navigate, flexible to manipulate, and robust to use in varied environments. Interactions with paper documents create rich webs of annotation, cross reference, and spatial organization. Unfortunately, the resulting webs are confined to the physical world of paper and, as they accumulate, become increasingly difficult to store, search, and access. XLibris [Schilit, et al., 1998] and similar systems address these difficulties by simulating paper with tablet PCs. While this approach is promising, it suffers not only from limitations of current tablet computers (e.g., limited screen space) but also from loss of invaluable paper affordances. In this paper, we describe PapierCraft, a gesture-based command system that allows users to manipulate digital documents using paper printouts as proxies. Using an Anoto [Anoto, 2002] digital pen, users can draw command gestures on paper to tag a paragraph, email a selected area, copy selections to a notepad, or create links to related documents. Upon pen synchronization, PapierCraft executes the commands and presents the results in a digital document viewer. Users can then search the tagged information and navigate the web of annotated digital documents resulting from interactions with the paper proxies. PapierCraft also supports real time interactions across mix-media, for example, letting users copy information from paper to a Tablet PC screen. This paper presents the design and implementation of the PapierCraft system and describes user feedback from initial use.