It calculates new 2D coordinates for the atoms on the canvas in order to get the same molecule in an evenly organized fashion.
Partial cleaning of a structure is possible, too. If you have selected fragments of molecules or certain elements of a multimolecular structure, 2D cleaning affects only these selected objects.
You can determine the 3D structure of your molecules ("clean them in 3D") by using the Clean 3D option on the General toolbar.
Cleaning feature is available only if the server connection is active, and the appropriate web service is available. Otherwise the Clean buttons will not appear.