I disallowed them from robots.txt, I realized that there are around 10000 duplicate urls, some how G indexed same page 6 times with different url. It could be my mistake, I did not find any answer yet. Anyway, disallow helped me to remove bad urls.
I also used remove directory from GWT to remove directory. Actually traffic is down another 20% after the removal.
I did not submit reconsideration request yet. Did you submit reconsideration request?