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Using C how to read the floppy drive boot sector (connected to USB port)

You might want to try re-explaining.  I've read this several times, and I'm not sure what you're asking. 

I want to read the FAT boot sector of a floppy disk. The floppy drive is connected to  a USB port

Are you not seeing what you want when doing a web search on something like "how to read the fat boot sector of a floppy disk using linux"?

yes

I don't have a working floppy disk to test out with Linux, but I hope these sites help you out.

FAT File System: http://www.c-jump.com/CIS24/Slides/FAT/lecture.html
C Progam that reads FAT: https://github.com/pda/cfat16
Floppy disk block device manual: https://linux.die.net/man/4/fd

Do you have any sample code you can share? Or tell us the errors that you are getting if any?