This paper presents a method for the virtual manipulation of real living space using semantic segmentation of a 3D point cloud captured in the real world. We applied PointNet to segment each piece of furniture from the point cloud of a real indoor environment captured by moving a RGB-D camera. For semantic segmentation, we focused on local geometric information not used in PointNet, and we proposed a method to refine the class probability of labels attached to each point in PointNet's output. The effectiveness of our method was experimentally confirmed. We then created 3D models of real-world furniture using a point cloud with corrected labels, and we virtually manipulated real living space using Dollhouse VR, a layout system.