Jayess,
Yes, there are hidden files on macs just like on Windows machines.
You can, in fact, reformat the flash drive to wipe it completely. In order to do this, open up "disk utility." (You can find this application on your mac under Applications --> Utilities --> Disk Utility)
Once Disk Utility is open, just click on your flash drive on the left hand side, then click on "erase" on the right side. This will bring up a menu allowing you to rename the flash drive and choose how it's formatted.
NOTE: If you want to use this with your windows machine, you'll want to format it as MS-DOS (FAT). You cannot see a Mac OS Extended (Journaled) partition on a windows machine.