|NTFS permissions are probably going to be your answer.|
are your users and computers part of a domain?
right click the folder(s) to which you're interested in restricting access, choose Properties, and click the Security tab. Most folders, by default, grant "Everyone," "Users," or "Domain Users" permission to Read and Execute things in those folders. If you remove this permission, people who shouldn't have access won't have it.
careful playing with permissions, though, if there is a service account that an application depends on and it is functioning based on these permissions, removing access may cause the application to cease functionality.