How to web scrape on a java scripted page

Question

Hi,

I am developing an application that will be used to web scrape in a way that when a button is clicked it will fill up a web form and then submit those values. Filling web forms and submit values is not an issue, but problem comes when java script shows message box for acknowledgement and other business validation messages. I am using a hidden browser control to access page controls and to submit values. Can anyone guide me how to cope with this kind of issue.

Thanks,
asif