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Right now, we're working to migrate our company sites for international markets to this scheme

www.company.com/[2 letter country codes]
www.company.com/uk    #for United Kingdom
www.company.com/au    #for Australia
www.company.com/jp    #for Japan
www.comapny.com/      #for united states, and non identifiable.

However, in google webmaster tools, we can geo-target each directory, but not the root. If we geo-target the root with US, all the other markets will inherit.

Is it better to move the US market to /us/ or leave it where it is?

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Is the primary market targeted for the US? If yes, I would leave it as is. The shorter domain will increase your hits on the SERPs and will allow you to keep whatever status is currently associated with www.company.com.

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I think by Geo-targeting all the other sub-folders you will be inferring the main top level domain be used for anything else and hence the US market.

I would not make a sub folder for the US.

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