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I am aware that you can delete Mac OS X hidden files/folders (such as /.Spotlight-V100 or .DS_Store) on a USB drive using various scripts. But then the hidden files/folders get added again before you eject it.

Is there any way to prevent this, and if so - how?

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Are you talking about specific files? – Oliver Salzburg May 26 '12 at 13:05
@OliverSalzburg the ones that OS X adds automatically. all of them. – gadgetmo May 26 '12 at 13:06
@Oliver thanks for the edit. – gadgetmo May 26 '12 at 13:08
It might be helpful if you put the names of the hidden files in your question. That way people will quickly know what you mean. – Oliver Salzburg May 26 '12 at 13:13
@Oliver thanks. done. – gadgetmo May 26 '12 at 13:19

To prevent /.Spotlight files you must prevent Spotlight fron indexing external drives.

To do this for a specific drive add a file called .metadata_never_index to the root directory of the removable drive.

You can also completely prevent spotlight indexing but I figured that was not what you were looking for.

To prevent .DS_Store files from being created:

defaults write DSDontWriteNetworkStores true

More Info Here (And More files that you can prevent) and Here

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