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I know that Java code is compiled into byte-code, that is executed by the JVM.
What is the case with C# ? I have noticed that applications written in C# have the .exe extension what would suggest they are native machine instructions. but is it really so ?
No.
Like Java, C# is compiled to an intermediary language (called MSIL or CIL).
Unlike Java, the IL is stored in EXE files which have enough actual EXE code to show a dialog box asking users to install .Net.