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answers:

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I am running windows server with asp.net websites and sql server 2008 and IIS 6. It is working fine.

Now I need to move my asp.net websites to another windows server and I have hard time setting correct file security for the new server.

Is there any way to compare or move or see difference file security between two servers?

A: 

Nice question, I have never think to do something like that :)

Use AccessEnum tool from sysinternals

http://technet.microsoft.com/en-us/sysinternals/bb897332.aspx

to see and compare your security access on your files and directories.

Aristos