Disclosed are editing tools for manipulating a three-dimensional (“3D”) data file or point cloud. An editing application may generate a visualization of the 3D data file or point cloud, and a user may invoke an editing tool over a particular region of the visualization that is rendered based on the positional and non-positional values of a first data point set and a second data point set from the 3D data file or point cloud. The editing tool may differentiate the first data point set from the second data point set based on unique commonality in the positional and/or non-positional values of the first data point set, and may edit less than all of the particular region by adjusting one or more of the positional and/or non-positional values of the first data point set while retaining the positional and non-positional values of the second data point set.