how can you, or can you even, deal with a monster den?

[Phantom]

the ones that are caves

[Mastima]

I'm confused. Are you asking how to destroy them? It gives you an explanation when you walk up to one. You use bombs that you have to make.

[Phantom]

no i'm talking the ones that are actual caves you enter and have no interaction with that I can find to destroy

not the nests... DENS

[Jocosity]

I'd like to know this too. I've cleared it out and looted every chest I can find, but it's still white on my map instead of gray. Is there just not a way to clear them out?

Edit: Nevermind, I cleared it. It turns out there in my case there were some chests outside of the cave too, and I had to loot those too for it to consider it cleared out. So just loot everything you can find and that should do it.

[Phantom]

Yup and some of them have chests that are so far away from it it doesn't make sense