would like to know if there is a way of killing all the "child-threads" on Windows and keep the main thread still alive.

As I tried to explain above, not unless you can get access to the real process ids.

The only ways I know how to do that is to use the forking open:

my $pid = open my fh, "/path/to/the/exe args |" ...;
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or the asynchronous spawn (

my $pid = system 1, '/path/to/the/exe args';
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rather than fork & exec.

Neither of which maps particularly well onto the fork & exec idioms typical of *nix code.