The cleaning features are available only if the server connection is active, and the appropriate web service is available. Otherwise, the clean buttons will not appear.
It calculates new 2D coordinates for the atoms on the canvas 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 by using the Clean 3D option on the General toolbar.