If your file system is NTFS, you could get into very big trouble when accessing the drive on psysical level, since much of NTFS is still undocumented and many structures change with every Windows version (or even service pack).

My idea would be to use WinHex scripting. I don't know if this works, but with the normal WinHex you can hex-edit files directly on disk when browsing psysical or logical disks. So I guess with the WinHex scripting system you could do the same.