Stop Addon Domains being Indexed in Shared Hosting Account

I have begun having some problems with addon domains being indexed such as maindomain.com/addondomain.com/page1.html

I never used to have this problem when running CMS systems like Wordpress and Joomla so I am guessing they created some rules in robots pr htaccess which stopped this from happening.

Any advice on how I can tell the search engines not to index addon domains in this manner. Of course I still want the other domains to be indexed just not on top of each other as they currently are.

did you try creating a robots.txt file in the folder maindomain.com/addondomain.com/ ? That might work

No but what would I need to put in it? I do not want to stop addon domains being indexed totally just being indexed under the main domain. I know this is possible because it only started happening when I built a site using pure html and css rather then using a CMS such as WP or Joomla which points towards htaccess or robots file having something to do with stopping this type of indexing.

You probably left your root domain exposed at some point and Google indexed them. They'll probably fade away after time once your main site is up.

I am looking into rewritecond a little more as I think this is what originally stopped it from being indexed on the other sites. Hopefully they will drop off in time too.