How to enable integrated fingerprint reader with fprint
apt-get install libpam-fprint dpkg-reconfigure -plow libpam-runtime # Enable fingerprint reader
Install the necessary packages if they aren't already present.
aptitude install libpam-fprintd
Observe that the needed lines in common-auth are already present.
$ grep fprint /etc/pam.d/common-auth auth [success=2 default=ignore] pam_fprintd.so
Log in to the desktop. Open a terminal. In the terminal run fprintd-enroll and swipe your right index finger five times. Now you should be able to authenticate by swiping your right index finger.
If you have an encrypted home directory then logging in from GDM by fingerprint does not work: the home directory cannot be decrypted. The solution is to log in from GDM with a password. (You encrypted your home directory so that even if someone has physical access to your computer, and it's turned off, then she can't read your files without taking it to the NSA. But if she's a bit clever and handy she can fool the fingerprint reader using a fingerprint lifted from the computer case.)
The problem is that GDM follows the default authentication procedure which starts with an attempt to read a fingerprint. Only once this fails or times out is a password requested. That is not convenient. To eliminate fingerprint authentication from the display manager login, edit /etc/pam.d/gdm or /etc/pam.d/lightdm so that it includes /etc/pam.d/common-auth-nofinger rather than /etc/pam.d/common-auth; copy /etc/pam.d/common-auth to /etc/pam.d/common-auth-nofinger and remove the line auth [success=3 default=ignore] pam_fprintd.so from the latter.