Remove overlappings

[alexeys85]

I have thousands of polygons that may partially or completely overlap each other. It is necessary to merge the overlapping ones so that the result doesn't contain a hole. If the result contains a hole, then I just subtract one polygon from the other to remove the common part. Simply speaking:
I do Union in pairs. If the result has a hole, then I do Difference.
It works, but it painfully sloooow. Probably there are faster algo?