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There is a simple Hello World Console Application. We compile it and get an assembly (EXE). The EXE is copied into 5 different folders and run from each of the locations. How many instances of the CLR are running when the 5 copied instances are running at the same time?”
Each physical process gets its own copy of the CLR because each is hosted separately. Thus if you create 3 instances of your .NET app you will have 3 copies of the CLR running. Each process will have at least one AppDomain. Where it gets sort of tricky is with domain-neutral assemblies. Domain-neutral assemblies, like some of the system assemblies, are actually shared across AppDomains. This reduces the footprint of the CLR.
check original answer at : http://social.msdn.microsoft.com/Forums/en-US/clr/thread/238c5f43-1d12-4c80-a987-0b8fdfd6d7e4