As a metaphor for the mind, an ongoing (and expanding) code is generally as good as any, in my view. So, if you had a code that apparently had as one of its core ends to keep being seamless/not visible, how would you program it?
For example imagine a program that does various stuff, but a major goal of the programmer is to keep those secret. So if some other coder opens the program, they should have great difficulty in moving past the surface. On the surface (again presenting a metaphor here) the program might just seem to mirror parts of the room the person who runs it has in their sight.
Of course there is another catch in this parallelism: the only actual "second" programer who would try to find what the program is, is the person whose mind the program is a metaphor of.
Anyway, in my view there always are ways to go beneath the surface, when a vast process is running it can remain invisible for only so long.