To hide a folder in Samba you must edit the smb.conf file (/etc/samba/smb.conf). To hide a folder globally put the following into the [global] section or into the relevant share section if it’s just for a single share.
eg. To hide Lost+Found in all Samba shares
[global] .... hide files = /lost+found/
Reboot the Samba service or wait for a minute until the configuration reloads automatically.
Open a share and check that the folder is hidden. This only marks the folder as hidden so if ‘Show hidden files and folders’ is ticked, the folder will still be visible but slightly transparent. Untick this option and the folder will be hidden from view.