If you can mount the hard drive on a Windows PC (either physically, or over a network), you can just instruct System Ninja to clean it like a normal hard drive.
I’m not sure if we understand. Should I download all files all the time. Clean them and upload again or there is interface to put FTP details and click on software application?
There is no interface to connect via FTP. System Ninja can only operate on mounted disk drives.
Of course; if the files have been serialized into the database, System Ninja will not be able to remove them. You’ll need to do that with an SQL query.