bubai, .conf files are usually plain text files so it is possible to edit them with any text editor.
but whether one should or not depends on which config file and what the outcome one is expecting.
can you please provide a specific example and maybe we can provide better assistance. i have in the past made alterations to grub.conf , httpd.conf , sshd.conf , ... eventhough they are automatically generated, doing something like manually disabling root login is usually preferble.
unspawn: i'll remember to check post count before making a sarcastic reply.