I have started a new site a month a go, I made some design mistakes and found that google has indexed about 600 empty pages of my site (which is very bad after panda), I am having very bad rankings and I think this is the reason behind it. I have added about 50 origianl content pages and made all empty pages return 404 (which is the fastest way according to Matt Cutts) now it's been 20 days since I added the 404 response and Not even one page is removed from the index???!!!! When I login to WMT I see 180 pages as not found (returning 404) but all of them are in the index, is there any way to speed up de-indexing of unwanted pages, they are really hurting my ranking.
404 error is just an intimation to the search engine about the non-existence of the web page... Though search engines claims that they will remove the web page from the index after discovering this error, but that will happen after next crawling. What you can do is, remove your pages manually from the index using URL removal tool in Google webmaster tools or redirect these pages to either index page of your website or any other relevant page.