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Canonicalizing http://sub.test.com to http://www.test.com will tell Google that those two individual pages are the same and it should only index http://www.test.com--it won't affect other pages on the subdomain. If you only have a few subdomain pages that are duplicates of root domain pages, you can just use canonicals to indicate which pages you want indexed. You won't need to noindex the duplicate ones--they will fall out of Google's index naturally once Google sees which are the preferred, canonical ones.

Thanks for your help Jesse - will just have to work harder