Internal porcessing of Framework

The .NET Framework class libraries are themselves written using managed code and are stored as shared assemblies in the global assembly cache (GAC).

Moreover, these assemblies have already been converted to native code using a utility called ngen.exe so there's no time penalty in having to convert them to native code 'on the fly' using the just in time compiler as there normally is with your application itself.

Apart from that, your application just loads the .NET Framework assemblies it needs and execution proceeds as it would do if you were using any other class library assembly.