I used
sudo apt-get purge [package_name]
and
sudo apt-get autoremove --purge
to remove an application so that on reinstalling it gets back to default configuration. But it didn't work, all previous modified configuration were still there.
On searching I found a dir in "/root/.[package_name]". Does apt-get purge remove config files stored in user home dir? If not then how to remove them?

apt-getnever touches the home directories, for a good reason. – Marco May 13 '12 at 8:54