I have used the google removal tool to remove just certain pages from their index that are no longer on my site, and I learned something...I use a custom 404 page so that if I delete soemthing or some other file is missing then the customers will get a handy menu so they can click back into my site instead of a scary server error message. When you use the URL removal tool it goes out and looks to see if the page is still there - it could care less about the content on it, just that it's there. When the custom 404 page comes up it thinks it found the valid content and refuses to delete the page (probably to protect you from sphincters trying to delete your site for you). The only way I could get it to remove my pages from the index was to disable my custom 404 page for a couple days, put in the delete request and wait till the pages no longer showed up in the SERPS. I even sent an E-mail to Google's technical support telling them it wouldn't let me delete the page and I needed help. The friendly customer service person argued with me that the pages were still there, even though he was looking at a page that had WHOOPS on it in huge letters and said the requested page was no longer present. So if you have a custom 404 file, beware when trying to delete pages.