If I recall correctly, in AE on a Mac, you did File > Import > File..., selected All Files from the pulldown menu on the bottom of the import dialog, then imported the .MOTN file.
Mac OS X cleverly presented .MOTN files to applications as if they were rendered Quicktime movies. When the app requested a frame, Mac OS X rendered it on the fly and returned it to the app. As such, they were flattened, not layered, so this may not get you what you were looking for.
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dang. didn't work for me. Ae gives me the option of importing multiple files in File/import, but it treats it like more than one element. it doesn't unpack the motn file. also tried selecting "all files" in the dropdown menu on the import window, but that still gave me a flattened file.
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