Yes you can
Simplest way:
Hang the files in your virtual file system. From hfs you can give access permissions only to files in the virtual file system, but you can't do it if they are inside a real folder.
If you are template builder:
You change the way comments are used and displayed, and you could use the filecomment to add some flag (that is never diplayed), and use this flag in the file section to decide with the 'member of' macro if the file should be added or not, if the %user% belongs to the group that is allowed to access the file.
