What should I do about not found pages?
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I took over a site that had been hacked. A bunch of pages were created that said domain.com/cms/viagra.
The pages are gone but they still show in webmaster tools as not being found, which is what I want. However, should I do anything besides leaving them as 404?
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In this instance, I would remove the URLs from the index. You can do that in GWT. The alternative is to leave them as a 404, but that isn't my preferred method. You don't want to redirect them because they are spammy pages that could potentially negatively affect other pages.
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How would you recommend removing them?
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Use the tool in GWT, Go to Google Index > Remove URLs