How to remove a partition on a USB drive?

Sounds like this is a customized U3 drive!

U3 is a technology that, along with functioning as a normal USB data drive, also can emulate a CD-ROM station.

The virtual CD-ROM partition can not be modified normally, and is not "burnable" in the traditional sense. However, it can be modified and even disabled with specific tools.

To remove the virtual CD-ROM drive, you would need an U3 uninstaller available at http://u3.com/uninstall [broken link, redirects to a different domain]

You should also be able to remove it under Ubuntu, with the help of http://u3-tool.sourceforge.net/ (I would recommend trying the latest version, the one that came from the Ubuntu repositories did not work on my U3 USB stick)

A note of warning though: The u3-tool above is not guaranteed to work on your specific drive, and may (though it has not happened to any of my drives before) mess it up. Use at your own risk. I would recommend using this as a back-up if the official U3 uninstaller does not work.

I had the same issue, but my USB drive seemed to be a branded Transcend Jet flash model for which I used this tool: CD-ROM_Remover_v1.0.0.3.rar (source)

For those who don't know the exact model of the drive you need to get the VID and PID of the USB drive and search it in a online database (similar to flashboot.ru)

PS: Make sure you also check the duplicate questions for additional ideas.