An invisible file (.DS_Store) maintains various information regarding the folder in which it is located (icon view and positions). On other systems, those files are visible (and completely useless). You can choose to remove them before burning a CD, for example. By default, this option deletes all .DS_Store files from the hard disk. After deletion of these files, the appearance of folder content will be reset, and all your folders will be the same as when the system and the applications were first installed.
From the Rebuild tab in the Maintenance pane, you can choose in which folders these files will be removed by clicking the Select button. You can choose to remove all the .DS_Store files of the selected folder and all its subfolders or to remove only the .DS_Store file of the selected folder.
From the Automation pane, all .DS_Store files will be deleted.