I don't think your files are corrupted. Your example line looks like it contains regular text with null bytes between each character. This suggests it's a text file that's been encoded in UTF-16 but the byte-order mark is missing from the start of the file. See http://en.wikipedia.org/wiki/Byte-order%5Fmark
Suppose I open Notepad, type the word 'filename', and save as Unicode Big-endian. A hex dump of this file looks like this:
fe ff 00 66 00 69 00 6c 00 65 00 6e 00 61 00 6d 00 65
If I open this file in Vim it looks fine - the 'fe ff' bytes tell Vim how the file is encoded. Now suppose I create a file containing the exact same sequence of bytes, but without the leading 'fe ff'. Vim inserts ^@ (or <00>, depending on your config), in place of the null bytes; Notepad inserts spaces.
So rather than remove the nulls, you should really be looking to get Vim to interpret the file correctly. You can get Vim to reload the file with the correct encoding with the command: