We propose Limpid Desk which supports document search on a real desktop with virtual transparentizing of the upper layer of a document stack in projection-based mixed reality (MR) environments. In the system, users can visually access a lower layer document without physically removing the upper documents. This is accomplished by projecting a special pattern of light that is calculated to compensate the appearances of the upper layer documents as if they are transparent. In addition, we propose two types of visual effects for users to cognize the progress of the transparentizing of real documents and to recognize the layer number of the virtually exposing document, and excecute psychological tests to confirm the intuitiveness of these effects. This paper also presents an intuitive document search interaction in the proposed system. Categories and Subject Descriptors H5.1 [INFORMATION INTERFACES AND PRESENTATION (e.g., HCI)]: Multimedia Information Systems. - Artificial, augmented, ...