As described in questions, if I see a file in unix then I see special characters in it like ^M at the end of every line but if I see same file in eclipse than I
They are probably Windows carriage return characters. In Windows, lines are terminated with a carriage-return character followed by an end-of-line character. On Unix, only end-of-line characters are normally used, therefore many programs display the carriage return as a ^M.
You can get rid of them by running dos2unix on the files. You should also change your Eclipse preferences to save files with Unix end of lines.