You ask for advice on how to refactor your script, but you don't appear to understand why to refactor it. Without the why, the how isn't going to do you much good. And with the why, the how may fall out quite naturally.
If your script is working perfectly and needs no modification and all you'll ever do with it is run it, then you probably don't have a reason to refactor it - and I say that from the perspective of despising long routines. But...
If something's wrong with it
If you are trying to find a bug in your 1,000-line program, you have some hard work ahead of you. The problem could be anywhere. Break it up into smaller pieces so that you can verify the input and output at different stages - ideally, write tests for the smaller pieces. Fine-grained unit tests will tell you what isn't working, the nature of the error, and where the error exists.
If you need to modify it
If you need to change the script to - say - accommodate a new graphics format, or take advantage of multiple processors, or record its activities to a log - you will find it easier to extend if the program elements that need revision or extension are better isolated.
If you're trying to explain it to someone else, or show it off
You will find it much easier to convey the ideas in your script to another developer if the ideas are broken out into discrete methods.
So, there are some reasons why you might choose to refactor. If any of them apply, refactor accordingly; the how will drop out naturally. Extract Method may be your best friend.