It's a good thing to ask questions. They form the way to think of the problem. I found my solution on sending the question:
Use a batch file to start the 16 BIT application
There is a "DOS" command in Windows XP (and later): TaskKill. Options:
/F force killing
/IM not PID but Name of programm
/T kill also sub-tasks (for my example wowexec.exe)
(there are much more not used here...)
Create batch file:
myprogram.exe
taskkill /F /IM ntvdm.exe /T