Microsoft Security Essentials is fairly fast at scanning for viruses, but it takes a long time to remove a virus. It would be much worse if the virus duplicated itself in many files.
I guess maybe MSE is doing some kind of house cleaning and repairing stuff (liking checking and restoring the changes that the virus probably made in registry). If that is the case, why does MSE do this for every instance of that virus?
Is there any workaround?