It might be that you are trying to use V1.1 ASPNET_REGIIS.EXE for V2.0 or V4.0
A unique version of Aspnet_regiis.exe is included with each version of the .NET Framework. Since each version of the tool applies only to its associated version of the .NET Framework, be sure to use the appropriate version of the tool to configure an ASP.NET application.
Refer:
MSDN: ASP.NET IIS Registration Tool (Aspnet_regiis.exe) [
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Open the command prompt and move to needed version framework path. Once you are in the needed framework folder, you will find related exe, use it.