Till now (docker version 1.12) we are using the following command to delete all the running containers(also, if we want to delete the volumes, we can do that manually using it's respective tag -v in the following command),
Delete all Exited Containers
docker rm $(docker ps -q -f status=exited)
Delete all Stopped Containers
docker rm $(docker ps -a -q)
Delete All Running and Stopped Containers
docker stop $(docker ps -a -q)
docker rm $(docker ps -a -q)
Remove all containers, without any criteria
docker container rm $(docker container ps -aq)
But, in version 1.13 and above, for complete system and cleanup, we can directly user the following command,
docker system prune
All unused containers, images, networks and volumes will get deleted. Also, individually i.e. separately, we can do that using the following commands, that clean up the components,
docker container prune
docker image prune
docker network prune
docker volume prune