In many cases you would want to make your storage unreadable for Storage Explorer or for other developers who use CBFS Storage library. Besides whole-storage encryption, you can use callback mode (read the details here).
In the callback mode, CBFS Storage doesn't write the pages of the storage to the disk but asks your application to perform operations with the underlying media (be it disk, network, memory etc.). When CBFS Storage passes the pages to the application for writing or requests the pages to be read you can transform the page contents in order to make the pages kept on the disk unrecognizeable by CBFS Storage engine.
With this approach, Storage Explorer will see garbage in your storage and your application will decode the storage and make it accessible for the engine.
You can apply any transformations, from XOR'ing the page bytes with some constant to swapping the page bytes to encrypting the page using some encryption algorithm.
Read more about callback mode here.