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Commonly on large ecommerce websites duplication between categories and sub categories is an issue. The views of search results can also be a factor IE: grid, list, etc- Association the sub categories with the main top level categories by using the canonical tag. It is also a possibility to block the /search/ results by using the robots.txt- search results aren't the most beneficial to the user and this is a ranking factor. The canonical tags are exceptionally effective for ecommerce structures.