Media Cleaner is a very advanced tool and should be used by someone who understands WordPress well. Then it will deliver amazing results. First, remember to backup your install (database and /uploads directory) before using this plugin. If you don’t know how to, I recommend you the UpdraftPlus plugin. You can also do this on your staging website if you use WPEngine for example.
The basic/recommend options for a first scan are those. I recommend you to consider Posts, Post Meta, and Widgets as a set. There could have been only one checkbox called Content instead of those three.
Start the scan, then wait. It takes time depending on your install. If it stops suddenly, please check how to debug Media Cleaner. When it is finished, have a look at the results and firstly, search for the images used by your theme directly (usually, the header, the hero, the logo). Those might have been detected by the plugin but it is not certain, as it is often used silently by your theme. Mark them as ignored if they are part of the results.
Check the files which were detected as not in use. Are they really not in use? Check a few of them randomly, at least. Then delete them with the plugin. They will be moved to the plugin’s trash and the database entry for the media will be also kept.
Use your website for a while. Everything works? Empty the trash. Many broken files? Restore them using the Media Cleaner dashboard, or your backup.
I recommend doing this after having checked your Media Library first. Now that your Media Library is clean, we would like to know which files in your /uploads directory are actually not registered as part of a media. I would preferably use the following settings.
All the files which are not part of a media will be detected. This makes sure that everything in your files is actually properly registered in your Media Library.
The combination of those two checks will make your install very optimized, sparkling. Everything is used and properly registered. Of course, this is ideal 🙂
Maybe you don’t really want, need or can perform a meticulous check of your install, and what you need is simply to detect the broken medias (which doesn’t have any files behind them). This scan will exactly require those settings.
Logically, doing this would actually detect all your media as not used by your system, since they are not checked against anything. But the Media Cleaner will recognize those settings and will display a message in your dashboard to let you know that it will only scan for broken media.