A mobile three-dimensional (3D) measuring system includes a 3D measuring device configured to capture 3D data in a multi-level architecture, and an orientation sensor configured to estimate an altitude. One or more processing units coupled with the 3D measuring device and the orientation sensor perform a method that includes receiving a first portion of the 3D data captured by the 3D measuring device. The method further includes determining a level index based on the altitude. The level index indicates a level of the multi-level architecture at which the first portion is captured. The level index is associated with the first portion. Further, a map of the multi-level architecture is generated using the first portion, the generating comprises registering the first portion with a second portion of the 3D data responsive to the level index of the first portion being equal to the level index of the second portion.