How to fix error 36 on AVI files?

Question

Hi I'm trying to back up a lot of avi files from an 500g IOMEGA External Hard Drive (MS - DOS (FAT)) to a 2TB WD My Passport External Hard drive (MAC OS Extended (Journaled)). Some of the files were copied from a friend's hardrive a couple of years ago, as far as I'm aware he is windows based, and some of these are the ones I am having trouble with copying.
The irritating thing is I can't copy anything without going through which ones have an error and which ones don't, I have been trying to copy the files through terminal as I watched this video - http://www.youtube.com/watch?v=6DLLQL7AvS0&feature=player_embedded and it did not work for me at all, it kept telling me it was a directory and did nothing.
Follwing that I tried the dot_clean command on the folder and it still would not transfer.
Finally I used the  rsync -av /path/to/source /path/to/destination command line, which started working but stalled at the first file I have been having problems with.
There is nothing wrong with avi file, it plays fine and as far as I can tell there is nothing wrong with the IOMEGA hard drive itself. I really want to back this stuff up and I've run out of ideas and I've searched everywhere for further solutions, I'm doing this through a MBP 2010 with SSD on OS X Mountain Lion 10.8.3. If anyone can give me an alternative way of transferring the files through terminal that will skip over the files with errors and then how to repair the files themselves I would be very grateful.
Thanks.

Answer 1

All I can suggest is using Data Rescue type software that will read the 1's and 0's of what makes up the files and rebuilds them from that, not what the corrupted file structure says.
Have you considered the files are tainted by malware or some sort of trick bag stuff?