Before running FileCleaner, be sure to back up your documents in case you later change your mind. In addition, try using FileCleaner on some test files until you understand how it works and what it does. Then you'll be prepared for the real thing.
You can use FileCleaner to clean up documents in two different ways:
1. One item at a time. You can do this by clicking the buttons on the FileCleaner Toolbar, which you can activate by selecting Toolbars under the View menu and clicking the FileCleaner checkbox. This is handy for cleaning up problems as you come across them while editing a document. Please note that this type of cleanup affects only the part of the document you are in. For example, if you are in a footnote panel, it will clean up the footnotes. If you are in the main text, that is what will be cleaned up.
2. All items (or several selected items) at once. Do this by selecting FileCleaner under the FileCleaner menu or by pressing the FileCleaner button at the left of the Toolbar. This option is useful for cleaning up all problems at one time. It is very powerful and is probably the one you will use the most. This type of cleanup affects the main text in a document, footnotes and endnotes, and (on a PC but not a Macintosh) headers and footers. It does not, however, clean up annotations.
When you run FileCleaner to clean up all items at once, the program asks if you want to clean up the active document, all open documents, or all documents in a folder. Select the option that suits your needs.