The command that you can use to format a pendrive or any other drive is "mkfs" .
The syntax is
mkfs [-V] [-t fstype] [fs-options] filesys [blocks]
Where the -V option will produce a verbose output on your terminal.
The important part is the "-t" options with which you can specify what kind of filse system do you want to create using the command.
For e.g. the windows follows filesystems "FAT" and "NTFS". Linux follows the filesystme "EXT3", "EXT4".
In case you want your drive to be recognized both in windows and Linux, it would be a good idea to use create a FAT filesystem. To create a FAT filesystem use the option VFAT with -t.
The "filesys" specifies the actual drive or the partition that you want to format. To get to know this you can use the command "sudo fdisk -l". or "df -h"
Note: sudo option is not required if you have logged in as root.
From either of the command find out the /dev/sd The will differ from one system to another depending on what you wan to format.
For eg: This is the output of df -h
Filesystem Size Used Avail Use% Mounted on
/dev/sda5 48G 33G 14G 71% /
none 986M 340K 986M 1% /dev
none 990M 480K 990M 1% /dev/shm
none 990M 84K 990M 1% /var/run
none 990M 0 990M 0% /var/lock
none 990M 0 990M 0% /lib/init/rw
/dev/sdb1 1.9G 4.0K 1.9G 1% /media/New Volume
If you want to format a pendrive it will be mounted in /media. So in the above output what we want is format is /dev/sdb1.
Thus the mkfs command would be
mkfs -V -t vfat /dev/sdb1