Run vs exec:
docker exec is used to run commands in an already running container. docker run is used to create a new container that can be committed to create an updated container.

Here is how execute commands inside a docker container as root:

$ docker exec -u 0 -it runningcontainer bash

The same concept works for docker run too:
Here is how execute commands inside a docker container as root:

$ docker run -u 0 -it dockerimage bash

This will clean up the /var/lib area:

docker system prune -a