Changing how the product thumbnail is displayed before adding to cart

In our fancy product designer, we have some template images that are used to help the user design their product in the way we need them to be designed. The issue with this however is that these template images are showing up in the image thumbnail in the cart. 

Is there a way to modify the thumbnail image before it gets added to the cart to remove those images/layers?

If you could at least direct me to which file is generating the thumbnail images in the plugin, that would be helpful as well.