A sort of straight forward way is to elevate the Z value of your Node2D to be higher than the tiles in question.
There are a variety of approaches, depending on your design. If you have something complex, maybe you need an algorithm to adjust these values of tiles and objects in real time.
Another method is to separate out what you want above the tiles into another CanvasItem (Node2D), or even create a new CanvasLayer for hold those nodes, and elevate the layer number.