I need to split an USB flash disk into two USB drives, each one with its own drive letter, but one of these has to be hidden.

In the non-hidden partition I want to place my software, and in the hidden partition I need to place some files that are required by the software in order to work.

Moreover, only the software may read, write, delete or execute the files in this partition.

I thought to use a little partition viewed as a CD-ROM drive, as they do in many flash drives, but this solution does not allow to write other data in a second moment, and it's visible to the user that can read the file.

Obviously the software must be able to access to partition and read, write, delete or execute the content.

Is there a solution to do so, possibly that work also on Linux?