I'm not sure if more people already know this, but I just thought I would share as I discovered this solution.
If you are tired of having to remove unwanted listings (you know...) from your mame list after rescanning, then there is a simple fix.
Go into your Mame INI config in mame (not MA), and update your rompath to have multiple folders. You do this by seperating each additional folder by a semicolon. Not sure how far back multiple rom folders go, but I'm doing this in 145.
For instance:
Find something that says in your mame ini:
rompath C:\directory
And set it like this:
rompath C:\directory;C:\another\directory
Then in MA, set your rom path to just C:\directory
Put all the things you want to boot up and be in your MA list in C:\directory and everything else in C:\another\directory (obviously substitute your file paths as you are using them). When you rescan your directory, you will only get everything in the directory you set in MA.