Should I remove 404 urls in webmaster tools?

[SamCUK]

I've recently removed a lot of category pages so should I remove the urls in webmaster tools or let them drop out of the index naturally?

[StreamlineMetrics]

I would recommend just letting them drop out of the index naturally. Google basically suggests doing the same thing - http://googlewebmastercentral.blogspot.com/2011/05/do-404s-hurt-my-site.html

If you find that the 404'd pages are still in the index after a period of time, then it may make sense to manually remove them via GWT.

[mememax]

I've always used GWT as a report on my 404, and since it stops on 1000 404s I always download them for further reference and then mark them as fixed.

404s are a natural response in the whole internet so fixing them is a good thing but waiting for google to remove them from your GWT account amy take long time. If they don0t bother you follow streamline's advice.