Aviva,
So this is more of a permissons question and how to scan with it.
You will need to create a user account that has limited access permissions.
So that the only places that user can access is if the share is open to 'Everyone'.
Then when you scan a target or server, just point it to the shares and use that account and it will ONLY scan what it can get to. It will scan what it can access and if its not accesible it will error out (no Access). Just make sure you configure the discover scans to NOT stop after X number of errors.
Good Luck
Ronak
Marked solved if possible