I tried to run the pruning script three times on the skeleton. But it didn't make further changes. The only changes were brought in the results, when the skeleton was pruned for the first time. After first time pruning, results of analyze skeleton was same.
I think the small branches (<6pixels) inside a skeleton, with no end point voxels, can't be pruned with this script. And that's why in pruned skeleton, all branches with one or two end points and less than threshold length were removed. But those with branch length lesser than the threshold value are still in the skeleton because they have no end point voxels.
What do you say about it?