The “Not Responding” message indicates that the extension is actually cleaning up the model. Models I’ve cleaned for others have taken upwards of a couple of hours to do. You can either be patient or you can take some steps to do some of the cleaning manually. Purging unused (Model Info>Statistics>Purge Unused) might help. Depending on how bad the model is, you might consider reducing the amount of things you have CleanUp3 do. Maybe take it in batches.
In the future, it would be wise to run Purge Unused and CleanUp3 periodically as you are modeling to prevent the model from getting out of control. I don’t know what your modeling workflow is but it’s likely there are other things you can do to help keep your model under control as you go so you don’t wind up with this sort of issue.