Update contact's field to empty value
I would probably create a profile with the website, and then use the 'update multiple contacts' to clear the website a hundred at a time (which is the maximum of contacts you can update with one profile action).

First you need to create a profile, and read up on profiles in the User Guide if you are not familiar with them.
Next you search for your contacts, and select a maximum of 100 at a time, and select the 'update multiple contacts' from the action list. You then select the profile and use the 'copy' functionality to set the website to empty.
I have not tried this, but this is what I would try to do if updating SQL is not an option.

If that does not work you will probably either clean them in the database OR delete the contacts and re-import (if that is an option).