If you want to clear an area of all resources, you can use the remove resources tool. However, you may only want workers to remove rocks to produce stone.
Once the collect stone tool is selected, click and drag over an area of rocks to mark them for removal.
Laborers, or any idle worker will help remove the rocks. The resulting stone will be moved to the nearest stock pile.
If the workers haven't yet harvested the rocks, you can cancel the work by using the cancel removal tool.