How Can I Deal With Overlapping Rectangles?

I am comparing two images and find the difference using compare_ssim, in that case I got the contours of differences, which i need to highlight by drawing rectangle around it, but

Solution 1:

This sounds like a problem for Non Maximum Suppression. Pyimagesearch has a pretty good article on it which I highly recommend reading. You can use the result of compare_ssim similar to how the article uses the result of the matching algorithm.