As always, CodeProject is your friend; here's one example of using C# to protect a folder: [
^]. I am sure you can find other C# examples if you search.
If you are looking for the equivalent of a complex file system on a USB drive with various Roles/Permissions/Groups, etc., then, as Philppe and Sergey commented, what you describe cannot be done, effectively. I suggest you focus on preventing folders/files you wish to protect from every being written to a USB drive; that may often not be possible without hardware modifications.
You can create protected files/folder on a USB drive; there's a variety of commercial software, like TrueCrypt (havne't used it mysefl), available: [
^], but, given an effort by a talented "hacker," that folder may be as insecure as most computer file systems are these days.
And, some USB manufacturers, like Kingston (for one), make a USB drives with extra security features: [
^].