"Manually" is a little better, because at least you're using your hands to move the keyboard and mouse to cause the files to be deleted. But it still suggests t

"Manually" is a little better, because at least you're using your hands to move the keyboard and mouse to cause the files to be deleted. But it still suggests the image to me that you're actually opening up the hard drive and striking out the data with a pen. It's also not as if I can think of a better antonym for "automatically".