You are trying to clear logical device E: and not physical device. Try doing the following:
call CreateFile() WinAPI function to open "\\.\PhysicalDriveX" where X is the number of the device (see Remarks in description of CreateFile function for information about how to open the physical device properly). Then use WriteFile API function to write 512 bytes at offset 0 of the opened device.
If you get permission denied error when opening the device for writing, you can take our RawDisk product (trial version will work fine for you) which lets one bypass this security measure of Windows.
upd: As for calling CreateFile from C#, see PInvoke.net.