Use find with sed.
With GNU sed:
find . -name "*ctl" -type f -exec sed -i 's,^M,,' "{}" \;
With BSD sed:
find . -name "*ctl" -type f -exec sed -i '' -e 's,^M,,' "{}" \;
^M in sed argument is a literal Control-M, not ASCII ^ followed M. Press Control-v and then M to enter it.