for this you will need following things
1) 54 LEDs. or 4 seven segment display

2) 12* 1n4148 diodes
3) 3 *470 ohm resistors
4) DS1307 real time clock IC.

6) Prefboard 
7) ATMega328 with arduino bootloader.
8)16MHz crystal.
9) two 22pF caps.
10) 28 pin IC socket for the ATMega328.

11)10 k resistors
12)acrylic sheet
basics
The circuit uses the ATmega328p micro controller (the same as the Arduino uno board) and the DS1307 clock IC. You can easily set/change the time by pressing the setup buttons. It can be powered on with  USB cable from your computer 
circuit diagram

TESTING WITH SEVEN SEGMENT DISPLAY ON BREADBORD
FRITZING IMAGE

NOW ITS TIME TO BUILD CUSTUM BUID MATRIX DISPLAY
first we need leds  u can use any kind leds. i prefer milky ones
how to turn ordinary leds to milky leds

 using a sandpapper we can easily turn normal led to milky ones

 do this for all leds
SEE THE DIFFERENCE

NOW LETS CREATE CLOCKS FRONT PANEL
for this we need a led frame so i created a 3d model 

this print is done by eazyfab.com
you can print ur designs ineazyfab
 you download this from here front panel
now lets make led display

 arrange 3 leds as row and 5 leds for column follow the picture

 black dot represent the corresponing leds of 7 segment display
connect all anodes together(common anode)


                                                        

 arduino codeclock