The fast and stable reconstruction of building interiors from scanned point clouds has recently attracted considerable research interest. However, reconstructing long corridors and connected areas across multiple floors has emerged as a substantial challenge. This paper presents a comprehensive segmentation method for reconstructing a three-dimensional (3D) indoor structure with multiple stories. With this method, the over-segmentation that usually occurs in the reconstruction of long corridors in a complex indoor environment is overcome by morphologically eroding the floor space to segment rooms and by overlapping the segmented room-space with partitioned cells via extracted wall lines. Such segmentation ensures both the integrity of the room-space partitions and the geometric regularity of the rooms. For spaces across floors in a multistory building, a peak-nadir-peak strategy in the distribution of points along the z-axis is proposed in order to extract connected areas across multiple floors. A series of experimental tests while using seven real-world 3D scans and eight synthetic models of indoor environments show the effectiveness and feasibility of the proposed method.