Yes, there is. Just not for the subtraction part. Check out the documentation on custom drawing as well as the drawing-functions of the CanvasItem class:
const COLUMNS = 7
const ROWS = 6
draw_rect(Rect2(0, 0, COLUMNS*100+20, ROWS*100+20), "#0000FF")
for x in range(COLUMNS):
for y in range(ROWS):
draw_circle(Vector2(60+x*100, 60+y*100), 40, "#FFFFFF")
That said, practice aside, there really isn't any reason to do it like that. Just use a Sprite or TextureRect. Then you can create the images in the image editor of your choice (including transparent areas) and directly use these in Godot.