You could go the route of a pop-up window, but I wouldn't recommend
it. You can't programmatically close the built in message boxes,
and they have strange consequences for the dataflow (ie. Don't behave
exactly as you would expect), as well as you need the user to click on
it to make it go away.
You could make a pop-up vi, but you'd have to make it reentrant in
order to have the rest of your program running while the vi runs, and
it would add a few complications.
I have used the method in the attached vi a few times for things like
this. You can show and hide the indicators only when the loop is
running too if you like.
Hope it helps.