Hi Faraz,
I’m facing a similar issue with 3D UNet segmentaiton of multiple organs, and I also haven’t yet found a solution to this problem. Take a look here for example:

edges.JPG748×345 28.7 KB

You can see in the predictions there’s some serious blockiness! Checking the individual outputs also gives good results, so I’m not sure where this is coming from.
Did you ever find a solution to this problem?
-Chris