Running external programs is done with open, system, exec, or "backticks" (the qx// operator). You can save some file manipulations if you don't write an intermediate file and then rename and modify it. User input can be read from STDIN. Here's a sketch,

for (1..25) {
    warn "File Exists: $_.txt\n" and next if -f "$_.txt";
    print 'My prompt message: ';
    chomp(my $input = <STDIN>);
    open my $fh, '>', "$_.txt"     or warn $! and next;
    open my $ph, '-|', $cmd, $input or warn $! and next;
    {
        local $_;
        while {<$ph>) {
            do_your_processing($_);
            print $fh $_ or die $!;
        }
    }
}
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You should see that this needs to be fleshed out by all your unspecified requirements.