Secure file transfer programs such as sftp and Filezilla should work without trouble on the CS&ECE systems.
If you are having trouble with sftp or similar programs, look in your .cshrc or .profile to see if you have any use statements. Either shift these use statements to your .login, or change them to be use -q. Either change should clear the problem.
use is intended for an interactive shell, and generates output when it runs. The output can interfere with the operation of non-interactive file transfer programs. use -q suppresses the output. Shifting the use statements to your .login ensures that they run only when you are in an interactive shell.