Software: USB without Arduino
Hardware: RapideUSB

Diagrams

Process diagram

Block diagram

Schematics

Forgive the crudity, I put just the essential components but you have all the base here: an ATmega8a, the USB connection, Level converter, Finger print scanner and a handful of switches.

Creation

Bill Of Materials

Reminder: basically all the USB part is a RapideUSB board, and all the other components are soldered on that same board (on the free space zone). For the detailed BOM of the RapideUSB go to its page.

Fingerprint scanner GT-511C1
- My old version no more sold and poorly documented https://www.sparkfun.com/products/retired/11836
- In case, the latest version https://www.sparkfun.com/products/13007
- Code sample https://github.com/mlaws/GT-511C1_Mega
- Doc GT-511C1.pdf
Micro controller : ATmega8a, form factor and mostly identical to ATmega328 but cheaper and with less memory but still plenty more than enough
Level conversion between main circuit (MCU, USB, leds,...) @5v and the Fingerprint scanner (3.3v) : eBay cheapo 1USD level converter
- Note: this fingerprint scanner bast*rd is 5v tolerant for the power pins but serial comm must be at 3.3v, so I put the whole module on 3.3v
3.3v made with a LM317
- R1=240 and R2=400
Buttons
USB connector
Vibrator module for haptic feedback when scan fails
Leds, cables, board, caps, resistors, ...

Code

On the git repository : https://github.com/AlanFromJapan/alanarduinotools/tree/master/Atmegaxx8/FingerPasswordKeyboard

Points of interrest

Keyboard mapping

I live in Japan and have a Japanese keyboard on my pc, means that the keys are mapped differently, and it's the software job to adapt and send the right code to the PC. Therefore in the keyboard.h file you can select which mode you work in to correctly map keys and codes sent to PC. Japan is the one I use, US should be ok provided you check a little.
Default keyboard mapping: http://www.usb.org/developers/hidpage#HID_Usage or direct link to PDF.
About that mapping problem for Japanese keyboard, the invaluable explanation detailed is here http://web.stanford.edu/class/cs140/projects/pintos/specs/kbd/scancodes-7.html

Pictures

If you wonder top wood is Pao Santo and sides are Magnolia, finish is shellac and yes I had some splinters while working the Pao Santo

Finger Password Keyboard