Edit the page with the popup you will see the module in the page builder.
NOTE: If the popup is on every page of your site it could be site wide and may be located in the footer or header instead of individual pages.
Hover over the popup module and you will see the X to remove. Click the X to delete the module.
REMEMBER: The popup may exist on many pages. Removing it from one page will not remove it from other pages. So you need to remove it from all the pages it exist on.
If you want to save your popup to reuse it again later. Before you delete it make sure to keep a copy.
Edit the popup module, and select Save As...
Give your module a name and click save. You can now delete the copy on the page.