So you want to copy them, but retain the folder structure they're in? How much of the folder structure do you want to keep? Just the last subdirectory? All the way from the root?
If your files still have Canon's naming format, you could search for IMG_????.*. If you've been renaming them with some non-consistent names, you'll need to do as Pete suggests.
One other possibility (which you'll need to perform for each drive), if you have a file name pattern you can use, would be to open a command window and, from the root of each drive, run "XCOPY filepattern [Dest_drive] /s -Y" The /s switch tells it to copy the directory structure; the /-Y says to prompt before overwriting anything. You could also use the "XCOPY pattern > files.txt" to create a list of the files that would be copied, then edit that into a batch file to copy the ones you want.