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I'm trying to free up some space in my Testing SQL Server. It has SQL Server 2005, 2008, 2008R2 and the compact or express edition. Since I only use lately the 2008R2 version, its not clear for me from the Program Files which of the older folders I should delete (if I'm doing this right?). I see folders named as (80, 90, 100, MSSQL.1,MSSQL.2, MSSQL.3, MSSQL.4, MSSQL10_50.SQL2008R2...)

I will keep the ones that has the 2008R2 obviously, but is there a better way to not accidently delete something that I'm not supposed to?

I'm using MS.Windows Server 2003 R2 Enterprise Edition. Thanks

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To properly remove any program from Windows you should be going through Add/Remove programs feature under the control panel. You locate the SQL Server Version you want to remove and uninstalled it.

Optionally you could also run the original installation media for the version of SQL Server and select to remove an instance.

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I strongly suggest to read Working with Multiple instance of SQL Server. If it is not interrupting at all STOP the SQL Server services which is not required its more safer approach. Microsoft has history of behaving incorrectly when instance is removed from server having multiple instances present. I have seen it multiple times

IMHO If you have multiple instances its more safer to use command prompt to remove SQL Server instance as compared to GUI. Below is the dummy script. You have to open CMD as administrator and move to folder where Setp.exe file is present and then run below script.

Setup.exe /Action=Uninstall /FEATURES=SQL,AS,RS,IS,Tools /INSTANCENAME=MSSQLSERVER

You can read about uninstall parameters from Books Online. You can also have a look at how to uninstall existing instance of SQL Server

If you want to remove SQL Server 2005 This support article is very well written

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