Plugin or steps to select visible portion of a layer in the image

Hi,
I need to get the visible portion of a particular layer in the final image.
Lets say i have 4 layers and some portion of each layer is visible in the flattened image i would like to get the portion from each of the layers. The input will be in xcvf format.

I will ideally want to automate this and output to file in some format looking like this,
Layer1 ---> Co-ordinates of visible polygon from this particular layer in the image .
Layer2 ---> And so on.

Any pointers on how to proceed with the script will also be helpful. I think brute force is to take each non-transparent pixel and and find the same pixel in all above layers if it is not found it will be added to the region . Is this my only option ?
Or something exists like selection from alpha combined with multiple layers ?

Or if there is a way to find out for an image with all layers visible which pixel came from which layer ?