I tried the standard DotNetObfuscator that comes with Visual Studio 2010 on my code.
I did not change any standard settings on the code. I am a little puzzled by the behaviour of this tool. I tried to compare the values by loading both assemblies in reflector.
Somethings have definitely changed, but I am stil able to read the method as it is in the original assembly. Is there some setting that I need to change, before using this tool?
Not sure what exactly you you saw, but public method names mustn't be obfuscated--by virtue of their being public they must remain callable by callers outside the assembly. Private (and possibly internal) methods could have their names obfuscated, as can implementation details within methods, but may still be readable with Reflector even if the names are odd. Various obfuscation tools may provide further features that help prevent the use of tools like Reflector, but may vary in their ability to generate verifiable IL or in other ways I don't particularly understand.
Obfuscation is not a means of encryption--it only slows down the reader.