If we want to model the dynamic and contingent nature of human social interaction (e.g. for the design of human robot interaction), analysis and description of natural interaction is required that combines different methodologies and research tools (qualitative/quantitative; manual/automated). In this paper, we pinpoint the requirements and technical challenges for constituting and managing multimodal corpora that arise when linking Conversation Analysis with novel 3D motion capture technologies: i.e. to robustly track multiple participants over an extended period of time. We present and evaluate a solution to by-pass the limits of the current standard Vicon system (using rigid bodies) and ways of mapping the obtained coordinates to a human skeleton model (inverse kinematics) and to export the data into a format that is supported by standard annotation tools (such as ANVIL).