I think if u were to drag your C drive and drop into your external hardisk, it will create only a shortcut instead of copy it. There are few options you can opt that I could think of at this moment :-
1. Copy folder by folder just as what you did when you do it with your pendrive. No point backup your Window system folder as it may not work by merely copying back. Just backup those data files that you created.
2. Using third party software such as Norton Ghost, etc to make an identical image of your hardisk... but the downside of this is you need to have the software installed before able to restore the backup.
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