change all the unix commands which i have used in my script

If you script is dependent on lots of unix commands that you're calling via system or backticks, then you probably need to rewrite a lot of it purely in Perl.

However, I've been very pleased with unixutils as a native port of many standard GNU utilities to Win32. If you're only relying upon tools included in that project, then you may be able to use them seamlessly with your existing script -- though there could be some subtle differences that won't work as you expect.