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Sorry, but cgaliher, have you ever even tried your own solution?<br />
DFS does not support indexed search via network. No, we cannot go about and use the server-based index for fast searching on DFS shares.<br />
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So my suggestion is to reopen the question.<br />
I would use the sharepoint spin-off search server, there is a free edition: <a href="http://www.microsoft.com/en-us/download/details.aspx?id=18914" rel="ugc">http://www.microsoft.com/en-us/download/details.aspx?id=18914</a>
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Sorry, but cgaliher, have you ever even tried your own solution?
DFS does not support indexed search via network. No, we cannot go about and use the server-based index for fast searching on DFS shares.

So my suggestion is to reopen the question.
I would use the sharepoint spin-off search server, there is a free edition: http://www.microsoft.com/en-us/download/details.aspx?id=18914 [http://www.microsoft.com/en-us/download/details.aspx?id=18914]

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@McKnife Thanks for the update
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Is there software out there that will let you search the &quot;domain&quot; and not have to select every server?
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Is there software out there that will let you search the "domain" and not have to select every server?

What is the best software for searching an entire domain

Active Directory (AD) is a Microsoft brand for identity-related capabilities. In the on-premises world, Windows Server AD provides a set of identity capabilities and services, and is hugely popular (88% of Fortune 1000 and 95% of enterprises use AD). This topic includes all things Active Directory including DNS, Group Policy, DFS, troubleshooting, ADFS, and all other topics under the Microsoft AD and identity umbrella.

Active Directory

Windows Server 2008 and Windows Server 2008 R2, based on the Microsoft Vista codebase, is the last 32-bit server operating system released by Microsoft. It has a number of versions, including including Foundation, Standard, Enterprise, Datacenter, Web, HPC Server, Itanium and Storage; new features included server core installation and Hyper-V.