When a two-dimensional (2D) traveling salesman problem (TSP) is presented on a computer screen, human subjects can produce near-optimal tours in linear time. In this study we tested human performance on a real and virtual floor, as well as in a three-dimensional (3D) virtual space. Human performance on the real floor is as good as that on a computer screen. Performance on a virtual floor is very similar, while that in a 3D space is slightly but systematically worse. We modeled these results by a graph pyramid algorithm. The same algorithm can account for the results with 2D and 3D problems, which suggests that deterioration of performance in the 3D space can be attributed to geometrical relations between hierarchical clustering in a 3D space and coarse-to-fine production of a tour.