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 area
you want to clear.
Select a lowly mason who will be your exclusive stone block maker and
assign him to the burrow.
Build a mason's workshop inside the burrow.
Use the profiles screen on the workshop to restrict the dwarves
that can work there to your chosen
mason. (You'll need to have a
manager 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.
When the menu is opened by selecting something on the map (such as by querying a building) you need to navigate the menu with + and -. This is so you can still move the main map cursor with the arrows.
On a full screen menu (like the military screen), use the arrow keys to navigate.
Best Answer
Label them with a note N when constructed.