Anyway how the program being called and how it executed, yo will need to manager if you're invoking it from the Tk program. You had not told in which operational system you're running that, but for UNIX like systems you should look at the functions fork, open, waitpid and POSIX signals.

If you have control of the program being executed (you can modify it's source code), this will be even easier.

Regarding the See IO::Select to try to use non-blocking reading.