How to stop google from crawling my repository?

 I have deleted organization and repo without thinking of the caached url by Google. Now we have our website up but Google still shows cached URL which is hurting our organic views on original website. 

Can anyone help in that case? Should I use google webmaster tool?

The Google Webmaster tools are, to my knowledge, the official way to see how Google sees your site and ask them to recrawl part or all of it. You may want to check out their help site for more information.