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Look into the rgbd_slam package to do 3d slam using rgbd sensor like kinect. I am not sure if its currently maintained(fuerte version) since there is a new version of RGBDSLAM v2 for indigo and hydro already out. If you have problems you should better contact the developers of rgbd_slam package.

Apart from that there is an octomap package that builds 3d occupancy grid maps. The map implementation is based on an octree.