A method and system of generating a two-dimensional map with an optical scanner is provided. The method comprises acquiring coordinate data of points in an area being scanned with a mobile optical scanner. A current 2D map from the coordinate data is generated. A copy of the current 2D map is saved on a periodic or aperiodic basis. At least one data registration error is identified in the current 2D map. The saved copy of the current 2D map from a point in time prior to the registration error is determined. A second data set of coordinate data acquired after the determined saved copy is identified. The second data set is aligned to the determined saved copy to form a new current 2D map. The new current 2D map is stored in memory.