These are the items you need:

27 LEDs
Soldering wire and rod
Jumper wires
Three 2N3904 npn transistors
9 220O resistors
3 22K resistors
arduino board
perforated circuit board
Bend the negative terminal (cathode) of the LEDs and arrange them on the mold wi
th the bent cathodes touching each other as shown in the photo. For those who do
not know, the negative terminal is the shorter one.
Solder the cathodes together on the points where they touch each other so as to
form one layer of the LED cube as shown in the photo. Repeat this three times so
that you have 3 layers.
Join the layers together by soldering the anodes (positive terminals). To effect
ively solder the anodes, use a crocodile clip to hold the upper layer in place o
r use a piece of cardboard like i did.
start with the 9 220 ohm resistors and then 3 transistors and the LED cube as sh
own in the photos. Once you have arranged all the components on the board, solde
r them
Solder wires from each resistor. These wires will be connected to arduino digita
l pins 2-10.
Connect the LED cube anodes to the resistors. One anode should go to one resisto
r. Check the photo
Solder a wire on each layer
Wire the transistor. The collectors of the transistors are connected to the thre
e LED cube layers. The emitters are connected to the arduino ground pin. The bas
es are soldered to wires that have the 22k ohm resistors soldered on them.
Connect the setup to the arduino using the configuration i have specified above.
The numbers represent which arduino pin the defined wire or LED cube column is
connected to.