I have a wordpress site on which I was using different URL convention earlier but changed it now, both kinds are valid but now all links use new convention but Google have still indexed my pages by the old way of URLs. I want google to first remove my whole website and then crawl and re-index it. I am using the webmaster tools, so by using the webmaster tools or some other way is there a way to make it happen.
Use a 301 redirect. Since you're using WordPress, get the "Redirection" plugin. http://urbangiraffe.com/plugins/redirection/
There's no need to do it. In fact, it's far too much work for what you'd get. Just have the old links point to their locations. It's easier, faster, and you don't lose your rankings (not to mention traffic) in the meantime.