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You can find the admin page of the plugin under Tools->Shortcode Cleanup.
Under any particular utility (replace, delete, wrap, freeze) all of your registered shortcodes, except native WordPress shortcodes, will be listed.
Additionally, for every utility except freeze, you can write in the name of unregistered shortcode tag and select that tag for processing. This is useful in the case that you have visible shortcodes left over after changing themes or un-installing a plugin.
The replace utility replaces the selected shortcodes with whatever text or html you provide. If you don’t provide text it will simply delete the shortcodes in question (that is, it will replace them with the empty string that you provided).
The wrap utility leaves the shortcodes untouched, but places the “before” HTML/text before them and the “after” text/HTML after them.
The delete utility does just what it says it does. It deletes occurrences of the selected shortcode.
You choose how to deal with the content contained in the selected shortcodes. If you select “Shortcode tags and content contained in shortcode tags”, the string “[shortcode]Content Blah Blah Blah[/shortcode]” will be deleted entirely, but if you select “Shortcode Tags Only”, the string “[shortcode]Content Blah Blah Blah[/shortcode]” will be replaced by “Content Blah Blah Blah”
The freeze utility replaces shortcodes with their current, static html output. For example, if you had a shortcode, [number_of_posts], that output the number of posts you currently have like this: “The number of posts currently on this blog is 7″, then using freeze on this shortcode would replace “[number_of_posts]” with “The number of posts currently on this blog is 7″. This content has become static, which means, that even if [number_of_posts] updated its number every time you added a post, the number in the static output will not be updated.