Find a piece of wood large enough to make a 4x4 grid of 2,5cm on.
Draw up a 4x4 grid of lines.
Make dents in all the intersects with a center punch.
Find a drill bit that makes holes small enough so that the led will stay firmly in place, and big enough so that the led can easily be pulled out (without bending the wires..).
Drill the 16 holes.
Your ledcube template is done.