I would like some directories and files to be hidden from view on command. What is the best way to achieve this?

I could have a separate encrypted partition but I'd rather have hidden files sorted within the directory structure I already have
I haven't yet thought of a clever way to do it with symlinking.
I have about 3000 directories and maybe 10,000 files, of which maybe 100 I want to hide from casual users of the laptop/portable drive. It doesn't need to be well hidden, just enough to stop a user aware of partitions.

To rephrase the question:

- how do I mix 2 file systems together?

how are those two questions at all related? doesn't read anythign like a rephrasing to me...

if you put a . at the start of a directory or file then they are "hidden" and standard views won't show them, add a "-a" to a command and they are there again. that's apparently what you actually asked for there... seems like you'd be better of just understanding file ownerships better and put relevant files in directories the other users do not have the right to read.

Sorry, I always had trouble with communication.

I'll start again.

An example. In it's first state the folder might look like this.

But then when I mount another filesystem (possibly encrypted) this directory structure is filled with new files and directories: