This is a good starter project for getting used to working with a vertical mill.
We'll cover how to create a perfect cube, chamfering, and position repeatability.
I made mine at TechShop.

Materials Needed:
Aluminum stock
A small, flat scrap of wood

Tools Needed:
Metal Bandsaw
Vertical Mill
Endmill for machining the faces of the dice
V-mill for chamfering the edges of the dice
Drill bit for drilling the dots
Machinist's square
Clamp to use as a stop on the mill's vice
Parallels
Marker (oil pencil is good, or use a permanent marker if you have a solvent with which to clean it off)

Step 1: Rough Cut Then Square Up the Workpiece

Cut your stock slightly larger (say .24") than the desired dimensions of your dice.

Before we can do the more precise milling aspects of this project, we need to square up the rough cut pieces so that each face of the workpiece is perpendicular to the adjacent faces.

You can follow my 'square up stock on a vertical mill' instructable.

Alternately, since we are milling cubes, it is possible to skip some of the steps since the dimensions of this workpiece can be somewhat simplified as follows:

Cut your aluminum stock roughly to size.

Mill side 1 per the instructable

Mill side 2 per the instructable

Instead of milling the side opposite to side 2, turn the cube so side 1 is against the solid jaw of the vise and side 2 is facing to the left. Use a machinists square against side two (the same technique as used when milling side 5 in the instructable).
Mill side 3.

Sides 1, 2, and 3 will share a common corner. This is different than the previously mentioned instructable where sides 2 and 3 are opposite each other.

If you're milling multiple dice, repeat the above steps for each piece, then you can cut them all to the final size at the same time without having to move the 'Z' axis when milling the last three sides.

Put the die in the vise with side 1 against the solid jaw and side 2 face down. Take a skim pass off of the top face.

At this point you can set the proper Z height as the desired height of the cube and machine the remaining unfinished sides using one of the already milled sides against the solid jaw of the vise and a second milled side against the parallel. This lets you machine all three dimensions of your cube without having to make a skim pass on each dimension before cutting the proper depth. Be sure to use the wood scrap whenever you have an unmilled side facing the movable jaw of the chuck.

Step 2: Calculate Depth of Final Cuts

Right now we have a workpiece that should have faces at 90 degrees from each other, but the size in the X, Y, and Z axes will each be different. We need to bring all of those dimensions to the desired dimension of our finished die.

In my case I was aiming for a 0.65 inch cube. Using digital calipers I measured the distance from the bottom face to the top face. This gives us the distance from the top of the parallels to the bottom of the end mill, assuming we haven't moved the Z axis of the mill since making a skim pass on the top face.

Subtracting our desired dimension from the current dimension of the die gives us the amount of material that needs to be removed.

.740 - 0.650 = 0.09 inches.

Step 3: Cut the Final Dimensions

Set the z axis dial to zero, then crank the height to the desired cut depth.

If machining to tight tolerances, we would remove that material in two passes, the first pass at .089 inches, then a finishing pass of an additional .001 inches. If you don't really care about being exact, feel free to just make one pass at .090.

You should always try to keep the most precise sides of the die in contact with the fixed jaw and the parallels of the vise as you machine down the rest of the die.

Machine each of the three dimensions of the cube to the proper dimension by milling one side, then rotating the die in the vise without moving the Z axis.

All three sides of our workpiece should now be the same dimension, giving us a perfect cube.

Step 4: Chamfer the Edges

Remove the end mill from the mill and install a countersink bit.

Position the cutter so that the mill is above the movable jaw of the chuck. The closer you can get to the vise in the 'Z' axis the better, since you will get a larger diameter of the cutting surface in contact with your workpiece. If just the tip of the countersink touches your workpiece, you will get a lousy finish. Lock your 'Z' axis.

Turn on the mill and move the piece in the Y axis until the cutter bites into the workpiece. Move the workpiece in the 'X' axis, removing the sharp edge between two of the machined faces of the die. If you want to create a bigger chamfer, push further into the piece using the 'Y' axis and make another pass. Once you are satisfied with the size of the chamfer, lock your 'Y' axis.

Park the cutting tool to one side of the workpiece, Turn off the mill and unclamp the vise. Rotate the workpiece so that an unchamfered edge is visible above the movable jaw of the vise. Turn the mill back on and make a pass across the workpiece in the 'X' axis. This should put the exact same chamfer on the new edge that you put on the first edge.

Repeat this process for each edge of the cube.

I found that since the countersink I was using had several flutes, the aluminum chips sometimes got pulled back around to the workpiece instead of being thrown clear, and would gall slightly on the first pass of a chamfer. Simply making a second pass without moving the 'Y' axis removed any galling from the first pass and cleaned up the edge nicely. Using a countersink with fewer flutes would have helped prevent the galling, but I did not have one on hand.

Step 5: Calculate the Dot Positions

We will need to divide the face of the die into a 3 by 3 grid, leaving a small border around the outside.

In this example I will leave a 5% border.

divide the total length of a side by 10 and subtract that from the length of one side. That leaves us conveniently with 90% to divide by 3, giving 30% for the width and height of each square of the grid.

We really only need to calculate three x,y coordinate pairs. Those three positions can be used to drill all of the dots by repositioning the die below the drill bit.

Top left:
   x = border + half of a grid square
= 5% + 15%
= 20%
= 0.13

   y = same as x
= 0.13

Top Center:
   x = 50%
      = 0.325
   y = same as top left y
      = 0.13

Middle Center:
   x = 50%
      = 0.325

   y = 50%
      = 0.325

Step 6: Rough Mark the Dots

Just to make sure the holes get drilled in the right spots, it is a good idea to mark the faces with a marker before drilling.

One rule you must follow is that opposing sides of a die must add up to 7. That means that 1 is opposite 6, 2 is opposite 5, and 3 is opposite 4.

Step 7: Drill the Dots

Attach a clamp to the fixed jaw of the vise to use as a repeatable stop in the x axis.

Clamp the die in the vise so that it is butted up against the clamp you just attached to the vise. Be sure that side '1' is facing up.

Use an edge finder to zero the X and Y axes over the top left corner of the die.

Swap a drill bit into the mill. The bit needs to be smaller than the size of the grid squares in order for there to be space between holes drilled in adjacent squares. I ended up drilling with a 0.1 inch bit, which was just about right for the aesthetic I wanted. I did use a long drill bit, and the bit did wander a noticeably due to deflecting. The shorter the bit, the more accurate your holes will be.

Center the drill over the die using the X and Y coordinates from the previous step.

Temporarily lock the quill at the bottom of its travel. Use the knee adjustment to bring the workpiece up to the drill.

Turn on the drill and begin to drill by slowly raising the workpiece. When you are satisfied with the size of your hole, stop raising the the workpiece, unlock the quill, and raise the drill bit away from the workpiece. You can now quickly repeat the depth of that hole by dropping the quill to its bottom position.

Drill out all remaining center holes (we just did side 1, do 3 and 5).

Move to the top middle X/Y position and drill out the two side holes on side 6.

Move to the top left X/Y position and drill out all of the corner holes (sides 2, 3, 4, 5, and 6).

Step 8: Polish the Dice

Place a 400 grit sandpaper on a flat surface and drag each face of the dice across it firmly until all of the curved lines from the milling process have been removed.

Smoothing down the points of the die just a little bit as well is probably a good idea to help prevent the dice scratching each other when they touch. Some marring is going to be inevitable over time, but this will slow down that process somewhat.