how do I flatten comments in Acrobat XI?

You can use the following JavaScript instruction that can be executed in the interactive console (JavaScript Debugger):

this.flattenPages();

This will flatten the comments, markups and text boxes.

If you have Adobe Acrobat Pro, go to menu View -> Tools -> JavaScript and click on "JavaScript Debugger" to open it.

To run the code, make sure the cursor is on the same line as the text. You can place it anywhere on the line as long as nothing is selected. Either of the two following actions will cause Acrobat to run the code.

• Press Ctrl+Enter on Windows, or Command+Enter on Macintosh.
• If your keyboard has a number pad, you can use the Enter key on the number pad without pressing the Control (Command on Mac) key.
  Macintosh's have the additional issue of keyboard configuration
  mentioned earlier.

To know more about JavaScript Console take a look at: http://acrobatusers.com/tutorials/javascript_console

You can use this free tool: http://abracadabrapdf.net/utilities-in-english/acrobat-utilities/abracadabratools_en/
Courtesy of JR Boulay

If you had a "Flatten" menu item, that was not part of Acrobat, so you (or somebody) must have installed a flattening command. There are a number of different packages available for free (e.g. JR's). If you have Adobe Acrobat Pro, you can use the flatten function that is built into Preflight: Bring up the Preflight tool (Edit>Preflight), then use the "Flatten annotations and field" in the "PDF Fixups" category:

Once selected, just click on the "Analyze and fix" button and your document is flattened.

Karl Heinz Kremer
PDF Acrobatics Without a Net
PDF Software Development, Training and More...
http://www.khkonsulting.com