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How to remove old Windows and Program Files from second HDD
So I recently purchased a Samsung 840 Series 128GB SSD. Got it installed and did a clean install of Windows 7. Got the User Profiles and Program Data moved to my old HDD so the SSD is used only for OS and applications. Problem is I still have my old Windows, Program Files and Program Files (x86) on the HDD. This is causing some programs to show up in the Start Menu, how I don't know. The programs are listed as there but you can't run any of them. I intend to reinstall these programs on the SSD but want to get rid of all the old stuff first. I want to remove these folders but for some reason I am having trouble doing so (i.e. permissions, ownership). I thought about just formatting the partition but that is out of the question as I just spent a ton of time getting the default location for User Profiles onto the HDD.
Is there anyway I can remove these three folders without formatting the partition. I need to keep the Users folder. I tried messing with permissions but didn't get anywhere. Please help!