See guidance below for completely wiping and restoring afresh any USB pen drive from anuy Linux command line/terminal. I often do this when pen drives become corrupted and stop working. In this example, the pen drive is /dev/sdb, but yours may be different,

sudo fdisk -l

This lists the disks/partitions. Remember the correct /dev/sdx name for the device. In this example it is /dev/sdb

You may need to unmount any already mounted partitions - e.g sudo umount /dev/sdb1, etc.

The following wipefs command will remove any existing file systems from the drive. If you do not have wipefs installed, install it using your package manager.

sudo wipefs --all /dev/sdb

At this point, all file systems have been removed, any data on the drive is technically still recoverable. To permanently wipe all data from the drive :-

sudo dd if=/dev/zero of=/dev/sdb bs=1M

This dd command should complete quickly. This writes zeros (the if = input file) to the of (output file), which is the device. The bs (block size) flag sets how many bytes to read/write at a time, the default is 512 bytes, but above it has being set to 1 megabyte (or 1,000,000 bytes).

OR, for a more secure version which writes random data instead of zeros :-

dd if=/dev/urandom of=/dev/sdb

This one can take a while.

The pen drive is completely wiped now. and all data is unrecoverable.

If you want to now create a bootable USB drive now in Linux from an OS ISO file, use the dd command again here, e.g.

dd bs=4M if=ubuntu-12.04.2-server-i386.iso of=/dev/sdb

The pen drive is now bootable, and no further action is needed if this is all you want to do.

Or, to create a blank pen drive for storage purposes, you could put the drive into a Windows machine and format there, which might be easier/quicker, but to partition the pen drive in Linux, continue below as below

sudo fdisk /dev/sdb

This goes into the fdisk program. You need to now input specific commands in the following order.

1. Option d - this delete partitions (this is not needed if you have used the dd command above on the device). Repeat for each partition if present.

2. Option n - create a new partition, just accept all the defaults (unless you need multiple partitions of specific sizes, most people won't)

3. Option w (write changes)

To create a vFAT partition (readable on Windows)

sudo mkfs -t vfat /dev/sdb1

Or, to create exFAT partition, use the following command instead:-

sudo apt-get install exfat-utils exfat-fuse *[if not already installed)*
sudo mkfs.exfat -n *volume_name* /dev/sdb1

When complete, Linux should auto-mount the device. If not, mount the device as below :-

mkdir /media/usbdrive Mount /dev/sdb1 /media/usbdrive