Tip: You can use Lunar Magic's Overworld Layer 3 Editing system to edit or create your own layer 3 images (castle bricks, fish, rocks) and apply unique effects per level via the Layer 3 Bypass in the main editor.
The original Lunar Magic application requires a header to be appended before it can edit the files. By using Header Magic, headerless ROMs can be opened and edited directly, without the need for a header to ever be appended. Unlike simple batch scripts, Header Magic will not simply create hidden copies of the file. It truly extends Lunar Magic to seamlessly support headerless ROMs.
To get it to work, drop the contents alongside the Lunar Magic executable and open the launcher.
Source code is public domain.
Doesn't seem to work on Windows 10 anymore, at least it fails on my Windows 10 machine. I had a Windows 7 user confirm it works properly for them, though.
Mod's note: Couldn't really test this tool much because it doesn't run on my system. I'm assuming it's not Windows 10-compatible. Telinc1 confirmed it's working on Windows 7, though. Nothing more I can do here, so approving it in good faith.