Won't the Perl code run in Unix (our code will be running in Linux machines) and Windows both??

Perl and many modules will run just fine in both environments, and there is lots of Perl code that is entirely portable to many platforms. But in some cases, care has to be taken to ensure portability. For example, you'll often see code that is hard-coded to use the forward slash as a directory separator, which works in many cases on Windows, but not all. If instead one uses the core module File::Spec or one of the more user-friendly modules from CPAN like Path::Class, they'll do filename handling in a more native way, and you should have much less portability issues. When picking modules, you can look at their documentation as well as the CPAN Testers Matrix for compatibility (e.g. this is the one for IPC-Run3).