Hi,
I haven't used a 'normal' flash drive for securtiy purposes so I can't help you with that. But I have used a dedicated security device called Dinkey Dongle. As I recall it was pretty easy to use and the price for 1 off in the UK is £12, so not dead expensive. I am sure there will be others available from alternative manufacturers, so it may be worth checking this option out as well as using a flash drive.
Here's a link for Dinkey:
http://www.microcosm.co.uk/dinkey.php[
^]
Good Luck with your project :thumbsup: