The easiest way to do this is through Windows own built-in format tool, reached by simply right clicking on the flash drive in My Computers and choosing Format.
Generally, it is a good idea to choose FAT32 as the file system, as this is compatible with the most number of platforms and operating systems. Make sure not to do a quick format, as it doesn't do a thorough wipe of the contents of your drive.
After completing the process, it’s a good idea to unplug and replug your flash drive again. If it looks like a smooth, clean new drive ready for new files and apps, then you’re good to go. If not, try reformatting again, perhaps with another file system like NTFS.