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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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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 com.apple.desktopservices DSDontWriteNetworkStores true

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

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