There is no automated way to find the hacker code. Someone will need to roll up their sleeves and put their sherlock cap on to find and remove the malware if any remain.
I worked on a similar issue this past week and were a few hidden back door scripts that caused the bad content in Google, as well as modifications to the .htaccess files in different directories.
You'll need to clear all these up, then submit a reconsideration request to Google (which takes from 4-10 days to clear up usually). See, http://support.google.com/webmasters/bin/answer.py?hl=en&answer=35843