Yes, you can stop macOS from creating these, but because each folder serves a different "service" (indexing, trash, and time machine), you have to disable them individually.
The most effective way to handle this for external USB drives is a combination of Terminal commands and a "kill switch" file.
1. Disable Spotlight Indexing (.Spotlight-v100)
Spotlight creates this folder to store search indexes. You can tell macOS to ignore the drive entirely.
The Command:
mdutil -i off /Volumes/YourDriveName
The "Kill Switch":
To make it permanent (even if you plug the drive into another Mac), create an empty file at the root of the USB drive named .metadata_never_index.
touch /Volumes/YourDriveName/.metadata_never_index
2. Disable the Trash Can (.Trashes)
By default, macOS creates a local trash folder so that "deleted" files can be recovered until the trash is emptied. You can bypass this by creating a file with the exact same name as the folder, which prevents macOS from creating the directory.
The Fix:
rm -rf /Volumes/YourDriveName/.Trashes
touch /Volumes/YourDriveName/.Trashes
By making .Trashes a file instead of a folder, macOS will fail when it tries to move deleted items there.
3. Stop Time Machine Prompts (.com.apple.timemachine...)
The .com.apple.timemachine.donotpresent file is actually a "flag" that tells macOS: "Don't ask the user if they want to use this drive for backups." It is usually a good thing to keep if you don't want annoying pop-ups, but if you want it gone:
The Global Fix:
defaults write com.apple.TimeMachine DoNotOfferNewDisksForBackup -bool TRUE
4. Stop Network/USB Junk (.DS_Store)
While not in your list, macOS often drops .DS_Store files (which store folder window positions). You can disable these specifically for external/network drives:
The Command:
defaults write com.apple.desktopservices DSDontWriteNetworkStores -bool TRUE
defaults write com.apple.desktopservices DSDontWriteUSBStores -bool TRUE
The "Clean Eject" Solution
Even with these settings, macOS is persistent. If you want to clean a drive right before you unplug it (especially before taking it back to your Synology or a Windows PC), use the dot_clean utility:
dot_clean -m /Volumes/YourDriveName
This merges and deletes those "AppleDouble" hidden files in one go.
Summary Table
| Folder | Function | Best Fix |
|---|---|---|
| .Spotlight-v100 | Search Index | mdutil -i off + .metadata_never_index file |
| .Trashes | Deleted files | Delete folder, touch .Trashes file |
| .Temporary-items | App swap data | Hard to block; usually cleared on eject |
| .DS_Store | Folder view | defaults write (Global setting) |
A small warning: Disabling Spotlight on a drive with 500,000 files means you won't be able to use the Finder search bar to find anything on that USB—you'll have to use find or ls in the terminal.
Are these files causing issues with your rsync script, or do they just look messy on the Synology side?