Disable USB removable hidden files

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

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?

The reason you can't rm that folder is usually down to two things: SIP (System Integrity Protection) on macOS or the fact that the Spotlight service is currently using the folder. Even if you are sudo, macOS will often block you from touching its core metadata folders.

Here is how to force it out.

1. The "Correct" Way (Using mdutil)

Instead of trying to delete the folder like a normal file, you should tell the Spotlight manager to erase the index for that specific drive. This clears the folder and stops the "Permission Denied" conflict.

sudo mdutil -X /Volumes/YourDriveName

• -X: Tells the metadata utility to "delete the index search store" on that volume.

2. The "Force" Way (Telling Spotlight to Stop)

If you still get an error, it’s because Spotlight is actively writing to it. You need to turn indexing off before you can rm the directory.

# 1. Turn indexing off
sudo mdutil -i off /Volumes/YourDriveName

# 2. Now try to remove it
sudo rm -rf /Volumes/YourDriveName/.Spotlight-v100

3. If you get "Operation Not Permitted"

If you see this even with sudo, it’s because your Terminal doesn't have "Full Disk Access."

1. Open System Settings > Privacy & Security.
2. Click Full Disk Access.
3. Ensure the toggle for Terminal is ON.
4. Restart Terminal and try the command again.

4. Preventing it from Coming Back

Once you delete it, macOS will try to recreate it within seconds. To stop this permanently on that USB drive, do this immediately after deleting:

touch /Volumes/YourDriveName/.metadata_never_index

Why it's so stubborn

The .Spotlight-v100 folder isn't just a folder; it's a root-level system directory protected by the macOS kernel. On modern macOS versions, even the "Root" user is restricted from modifying certain system paths to prevent malware from hiding in metadata stores.

One final trick: If the drive is external, sometimes the easiest way is to eject it, plug it into your Synology, and run the rm -rf command from there via SSH. The Synology doesn't care about Apple's SIP protections and will delete it instantly!

Did the mdutil -X command work, or did you get a specific error message?