Visit Skin Editor → HTML, and select a Template that currently includes the Box you wish to delete. Locate the Box within the Template.
Or, if the Box does not currently appear in any Templates, you can simply select it in the Box Manager (i.e., where it says “Select a Box to add”), then click the Add Box button.
Once you’ve located the Box, shift + drag it to the Delete Box area on the right side of your screen:
Click Save Template to preserve the change.
Proceed with caution! As the warning in the Delete Box area suggests, this action will cause the Box to be deleted from ALL templates where it is currently used.