You'll need to find the usb_desc.h file and edit it. See the comments at the top of that file for instructions.
If using Windows, you'll also need to find software to remove the prior info about the device from the Windows Registry before you make each attempt at changing usb_desc.h. This isn't an issue on Mac and Linux, so it's usually easier to use those system for testing.
Also keep in mind, if you remove the HID-based serial emulation, Serial.print() won't work to the serial monitor, and Arduino won't be able to ask your board to reboot. You'll need to press the button for each upload. If you want to print info about what's going on, using Serial1 with an USB-serial adaptor can help.