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Since FMR is really working like a video, I do not think it is possible to have the mouse cursor not showing, as is the case for most screen recording applications.
Just wondering if you couldn't capture in Automatic mode (demonstration), where you can delete the mouse object if necessary, and then export to FLV or F4V? AFAIK that format can be imported in AE (as can SWF).
There seems to be an option for me in the Recording Preferences to not capture the mouse pointer. Does this not work?
Click Edit > Preferences > Recording > FMR and clear the option labeled Show Mouse in Full Motion Recording Mode
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Thanks ya'll, appreciate the help =)