This question has been asked before. I think it deserves a simpler, more direct answer.
Edit: - Please post answers specific to Windows platform. No one wants to install Ubuntu just to format a flash drive.
Use format in diskpart. For example:
diskpart
select volume E:
format fs=FAT
Note that the maximum volume size of FAT (as per diskpart allows, at least) is 4GB.
I'm sure there lots of ways to do this. One simple method i used was to partition my 16GB flash drive, created a 1GB and formatted it as FAT16, all done within MiniTool Partition Wizard.
This has been asked before. The answer is mkfs.vfat -F 16 <device>
It does not get much more simpler than that.
You could use a program such as this: http://www.disk-partition.com/free-partition-manager.html which in my opinion is the best partition manager (even the free version) it's easy and simple to use.