On the Cubby desktop application, click the X next to any cubby that you no longer want stored on the cloud or synced with other devices.
This stops all Cubby functionality for the chosen folder. Nothing is deleted from your computers or devices.
Tip: By deleting a cubby you are also freeing up space (assuming the cubby was syncing to the cloud). That is, a deleted cubby no longer counts against your space quota, though it may take time for the change to be reflected in the space indicator.