Many websites do not have just the one domain and will have sub domains as well, although the website sits on the main domain the sub domains can also be tracked by Google so how do you stop Google searching for these and stop them appearing on the search engine results.
In many aspects Google sees each sub domain as a unique site and one of these is how the URL removal requests from their index are treated, to remove these sub domains you will need to verify each of them with Google Webmasters tool and then remove them individually but as they also have their own root document you will also need to ensure that the robots.txt file of each sub domain disallows the related domain as a 404 error page is not enough as this can still send out the files that are underneath this page. Once all of the robots txt files are blocked for your sub domains then you can remove the individually using your Google Webmasters Tool accounts.
The thing about this is that you are not the first person that is having this problem and you certainly won't be the last, Google are aware that this matters needs to be attended and we are sure that it will be solved but for now the above is the only way to do this.
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