I am afraid that there may not be an easy answer for this.
If you were on Selenium 1 or Selenium 2 then I could have suggested to use AutoIT in case of java.
I dug up one post on SO about it, though not sure how much help it would be for you -
http://stackoverflow.com/questions/6668141/interacting-with-a-pdf-popup-in-seleniumDo let us know if you find any other solution.
~ seleniumtests.com