Image process (stacking) suggestion?

I am trying to make a image something look like this, (stacking one on top of other one)

And as for the starting point, I have an image of each level. as shown blow .

Here as you can see, some of area does not show the clear image of the flame, thus I want to cut that part out. (enclosed area with a rer line - I draw this line to show which area I want to cut).

Since there will be 100s of images look like this, I can not manually do that. So I wonder, is there a easier method of cutting this kind of non-necessary area in images.