You can just right-click and choose to remove any folders that you imported from Aperture. Or, if what you really want to do is completely start over, you can choose file->New Catalog and create a new empty catalog.
Thanks. I am a bit confused on the catalog file though.
I am going to use the LR >> Aperture plugin, so after I delete the Folder "LightRoom Masters", (which was created in the first Migration of Aperture), do I need to do anything with the existing Cat file or will LR create a whole new one for the new Aperture >> LR conversion.
The new catalog will have no images in it until you import. And if you use the Lightroom/Aperture plug-in it should work just like it did the first time. This is a new, completely separate catalog. You are starting over.