I am trying to rename the \"codesign\" file name for patch problem, but I tired everything and seems like I can only have read access to the filea inside usr/bin
Have you upgraded Mac OS X to the "El Capitan" version?
If so, you can't modify anything in /System, /bin, /sbin, or /usr (except /usr/local) anymore, even using the root user. They are calling this "feature" as "System Integrity Protection".
I had the same problem and found this explanation here.