Thanks for the pointers. I have found that the directory is changing to the correct vobs directory to run the ClearCase script by checking the working directory before calling  open(FILES, "cleartool find . -nxn -ele \"version(/main/$branch/LATEST)\" -print |"); but the script still calls it from outside the vobs directory. Must be something to deal with the open command how I can calling the cleartool find script.