Turn them into rock blocks (since a lot of blocks will go into a single bin in a storage room and that's much neater).
Clearing every stone takes a long time, but you can clear certain areas using burrows: Designating a burrow over the areayou want to clear. Select a lowly mason who will be your exclusive stone block maker andassign him to the burrow.
Build a mason's workshop inside the burrow.
Use the profiles screen on the workshop to restrict the dwarvesthat can work there to your chosenmason.
(You'll need to have amanager for this.)
Set make rock blocks to repeat!
Your lowly mason will dutifully go about their business selecting only stone from the burrow and will automatically take breaks to sleep and eat, so this is a pretty low-maintenance method.
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another method is using the quantum storage trick/bug/cheat first, create a 1x1 refuse zone
( i , move to were you want it, Enter , Enter ) and designate it as g arbage zone.
Now, you can select the area (any size) to dump in that zone ( d , b , d )
All items selected in the area will be hauled into that zone.
now, if you want to reclaim all the items in this zone, you can do it by using d , b , c , Enter , Enter
right on that zone
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Yet another option is to just hide the stones via d -> b -> h .
This only doesn't display the stones anymore, but they're still there!
Best used if you want your fortress to look nice quickly, without generating any jobs.
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Designate a stone stockpile ( p , s ).
Your dwarves will automatically move any available stone to those.
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Usually I use the quantum storage method, with an atom smasher to clean up the mess, but there are some other tricks: To clean out a storage room, build a catapult and have it hurl rocks at the wall.
That way you're also training your siege operator.
They can be a bit silly about where they get the rocks, but usually they'll take the closest one.
Build floors where your rocks are, out of the same kind of rocks.
Unfortunately this needs a little bit of micromanagement, as dwarves will suspend a job as blocked if the spot has a stone on top of it which is earmarked for a different floor square.
But they'll still do most of them, and you can go back and clean up the suspended jobs later.
If you're willing to waste some Z-space, build your rooms or tunnels by channeling, then build floors, The rocks will fall to the level below, and you'll have a nice clean area.
(You've now got a space below with 2 rocks in it, but it's out of the way.)
Remember that if you have stones marked for dumping, they won't be moved by dwarves trying to construct on the site.
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Similar to the quantum stock pile, I placed a refuse zone over a pond and it seams the items dumped there fall to the bottom.
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How do I collect rocks etc that are laying about in tunnels I've dug in Dwarf Fortress?
How do I collect rocks in Dwarf Fortress?
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Turn them into road blocks, build a workshop inside the burrow or designate a stone stockpile. You can also try building your rooms by tunneling. You can turn them into rock blocks or build a mason's workshop inside the burrow.  Another option is to just hide the stones via  d  ->  b ->  h  or designate a stone  stockpile  ( p , s ).  You can also use the quantum storage trick/bug/cheat with an atom smasher to clean up the mess. There are also some other tricks: To clean out a storage room, build a catapult and have it hurl rocks at the wall.  Similar to the quantum stock pile, you can place a refuse zone over a pond and the items dumped there fall to the bottom.
You can turn them into rock blocks . Build a mason's workshop inside the burrow.   Another option is to just hide the stones via  d  ->  b ->  h  or designate a stone  stockpile  ( p , s ).   You can also use the quantum storage trick/bug/cheat with an atom smasher to clean up the mess. There are also some other tricks: To clean out a storage room, build a catapult and have it hurl rocks at the wall.  Similar to the quantum stock pile, you can place a refuse zone over a pond and the items dumped there fall to the bottom.