I came across a Samsung 32GB USB drive. When I plugged it in, the partitions were a mess. Here's what I did

Format your disk from the Terminal using diskutil command, for example:

Partition using diskutil:

diskutil partitionDisk diskN GPT JHFS+ "My External HD" 0g

Erase boot sector with zeros (make sure you won't erase the wrong drive!):

sudo dd if=/dev/zero of=/dev/diskN bs=1024 count=1024

Warning: Above commands wipes all data on /dev/diskN, so make sure you've it correct!

Unmount the drive (replace diskN with your drive):

diskutil unmountDisk force diskN

List all drives:

diskutil list

Source: Disk Utility fails to erase/format an external HDD at reddit.