is it near base or out in the middle of nowhere

Obviously yes. That shi will always be there even when it turns to grass. It's best to acknowledge and fix your mistake rather than ignore it.

close only the top and put torches inside

nah i always leave them, execpt these few in my house that i turned into a mine

I'd either 1. Turn it into a mini quarry 2. Grab wool and turn it into a landfill 3. as others suggested, fill it up but make the inside hollow