i did something similar at home: let's say i have a folder called 'mp3' which i want to prevent access from other users, except me.
then as root:
chmod 700 mp3
chown rockmanexe mp3
now only my user account 'rockmanexe' (and root of course) can access those files and subdirectories created within. If another user want to access via konqueror or command line, a 'permision denied' message appears
This could only apply to user's home folders tho, i don't know how to prevent access to the entire system folders, but by default users can't modify system files.
Hope this helps