In vi, or at least vim, you should be able to issue the following command in command mode to remove them. 
:%s/^M//g

[download]
Where ^M is entered by hitting CTRL-V then CTRL-M (you'll see it shows up the same as the offending ^M's) Often systems will also have a dos2unix command. (others above have pointed out how to remove them using perl)

In reply to Re: can't see ^M to process. by cowboy
in thread can't see ^M to process. by DougC

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