Help to Format a USB pendrive
In order to re-use the pendrive after installing Ubuntu, just format it completely (including MBR) using gparted in linux or Disk Management in Windows.
Format the pendrive with gparted (in linux)
gparted comes with the Ubuntu flavour iso files, and are available in the live session of the desktop installers, 'Try Ubuntu'. It can easily be installed into an installed Ubuntu system.
In the top right corner you select which drive to edit. You can use the size and device ID to help identifying the pendrive. Be completely sure that it is the correct drive, and not a drive where you have valuable data !!!
Select the pull-down menu Device -- Create Partition Table...
Normally it is good to create an MS-DOS partition table in the MBR. After that you can select the unallocated space, right-click and create a new partition. USB pendrives are formatted with FAT32 to be accessed by all operating systems. Select a good label (a name), so that you recognize the pendrive easily in file browsers (Explorer). Click on the green tick to apply the edit operations.
Restore the pendrive to a storage device with mkusb or mkusb-nox
Install mkusb or mkusb-nox with the instructions at https://help.ubuntu.com/community/mkusb.
Wipe menu of mkusb
Manage the work via the wipe menu of mkusb
Manage the work via a command line with mkusb-nox
sudo mkusb-nox restore
Wipe the first megabyte - only in special cases
gparted should have no trouble formatting a bootable USB - that's only a concern with programs like grub-install, before the MBR is formatted. So you need not wipe the first megabyte for normal usage of the pendrive after it has been used as an installer.
In some special cases you you might need to Wipe the CD file system and then format it with gparted, or better: If you select another option in the wipe menu, it will wipe the first megabyte and create a new partition table and file system automatically.
Wipe the whole pendrive - only in special cases
Generally, we are warned that writing to USB pendrives will wear them down, and the lifetime is shorter than that of hard disk drives. This is true, but there are cases when wiping (writing zeros to) the whole drive helps. It reduces the risk of 'gridlock' and can also increase the write speed. See this link for more details.