Is there a way we can filter our the invoices list that is shown in the list view using script. I understand through customize view we can make our own search. But I have a very complex requirement and it is very hard to make it via search.

Which list view?

When you go to Transactions->sales->createinvoice->list

I dnt think so!

oh..okay thank you

You can not add code to to list views. The only way is to develop your own suitelet with all the functionality you need.