Filtering is a function of user accounts:
Option 1, give each user their own "home drive" to store stuff on… this makes tracking people easy and the "home drive" is a simple script that makes each user a folder with their log-in name and maps it as a drive when they log on. There could be privacy issues here but best practice is to allow at least one Admin account control over these 'home drive' folders so that they can be removed/ edited when people leave the company or "accidently" download porn… Muppets will be Muppets after all!
Option 2, look at your file structure and break it into groups… this really should have been done when you first set the system up but the basic idea is to make this example 1; folder/ drive available to everyone in the help_desk group and the example 2; folder is for people in the accounts group. If the file server just has 350 people all in the one group then IMO its past time to take a hammer to it and build a new file server.