In this paper we present an efficient method for aggregating binary feature descriptors to allow compact representation of 3D scene model in incremental structure-from-motion and SLAM applications. All feature descriptors linked with one 3D scene point or landmark are represented by a single low-dimensional real-valued vector called a prototype. The method allows significant reduction of memory required to store and process feature descriptors in large-scale structure-from-motion applications. An efficient approximate nearest neighbours search methods suited for real-valued descriptors, such as FLANN, can be used on the resulting prototypes to speed up matching processed frames.