Using SSH would be a good way to do that. You could log in as root, ‘cd’ into “/usr/local/apache/conf”, run “ls” to view what files are in there – and then you can ‘mv’ any files you don’t need to another location.
You could also use the Webmin file manager to do that too. You can log into Virtualmin as root, click Webmin -> Others, and there you can move around the filesystem and move/delete files you don’t need.
-Eric