Well I personally use Asia81's PackHack aka HackingToolkit3DS to extract my CIA files. I'm not sure how Wine works but you could probably follow this.
so its been a couple of hours me trying to figure this out i do manage to be able to use the Ctrtool now but now i am not sure if the tool is extracting or not i am guessing its not cuz i waited a couple of mins and no file was created and its seems everytime i use the command it just resets the tool ur assistance so far was apperciated @KunoichiZ but now i will need assistance regrading ctrtool extracting on mac i will just have to wait for someone with mac support