How to remove custom fields from the selector?

To hide meta keys from the custom fields form you need to prefix the keys with an underscore, such as _thumbnail_id.

To remedy your problem you will need to edit all of the keys in the DB to prefix with an underscore, then you’d need to edit all references in your code. Which is a bit of a pain to do. Perhaps there is a plugin which could help, but not that i know of.