If you need to clean up the hosting server and clean install is not an option and you know that all domains on servers were created with virtualmin you can remove all virtualmin domains in one shot using command line API:
virtualmin list-domains --name-only | xargs -n1  virtualmin delete-domain --domain
Wait a while and you are done. There are tons of useful options for command line virtualmin that you might want to explore if you are using virtualmin for your hosting domain management.