If you are having trouble with subdomains in Google Search you may be able to remove them.  Sometimes you end up with a lot of subdomains your client is unhappy with.  However, you can still remove them.  Domains and subdomains are unique and how they are treated could differ.  It is important to process URL removal requests within the index of the site you want them gone from.

You will need to remove each subdomain you no longer want in Google Search.  You will first have to verify them through the Webmasters Tool, and then work on individually getting rid of the subdomains.  This can take a while, and should not be done all in one day.  The subdomains have their own document root which is why you also need to look at the robots.txt file.  This will need to say disallow to get them removed.

By entering the robots.txt file you can tell the search bots what you want crawled and what should not be crawled.  Once you remove the subdomains you have to make sure you put the disallow in for that subdomain, otherwise it will just reappear in the search list after all your work.

For more information you would be advised to talk to a search engine optimisation expert.