what's the best way to get rid of unwanted Stone and other materials?

[Brother Crab15]

^^^^

[Astralis L.]

Mine it. But then you'll have a hole. You can fill-in holes with dirt.

[Runak]

Make concrete from granite and gneiss/basalt. Grind sandstone into sand for glass. Make quicklime from limestone. Convert compost to compost fertilizer (can be stored in chests but requires specialty in fertilizers).