How to remove or hide Apple applications from my app folder?
You can hide files from the UI using chflags command.
Assuming you want to hide iBooks app, start your terminal app do the following:

$ cd /Applications/
$ sudo chflags hidden iBooks.app


And you are almost done.  Start finder app and in Applications folder you won't see iBooks app.  But it's still in visible in the Applications Dock folder.  You have to restart Dock app, so the last step is to:

$ killall -1 Dock


and you are done!

You won't see the hidden app in the Dock or Finder.  It will be visibile to you from the terminal when used ls shell command.

Quick note, to unhide app just use the following command:

$ cd /Applications/
$ sudo chflags nohidden iBooks.app


Notice the nohidden flag. Previously we used hidden