Kyle, the cuts are made freehand with a scrollsaw. The article Jeff pointed to is a great start.
Technically, because the cuts are through cuts, the aluminum is not an inlay but a segment. With "Unravelled" I have a pattern that I tape to two sides of the blank. There are a total of 8 cuts with a glue up between each cut. It is not terribly difficult, just time consuming, although cut # 8 does seem to have a bit more pressure associated with it than cut # 1 :wink:
One of the keys to this and many types of segmenting is to match the kerf of your blade to the thickness of the material you are inserting. Basically what you take out you need to replace. In that pen I use 30 gauge aluminum which is 0.010" thick and so I use a scroll saw blade which is 0.011" thick (the difference of 0.001" is not really noticeable

)
I'm guessing though that your question is more to do with the shape of the cuts. A segmented layer through a square blank can look very different once the blank is turned round. The way I developed most of my patterns was to make cuts in what I thought would be a nice pattern and then turn them round. Along with the occasional pleasant surprise there were many "well that didn't turn our the way I thought it would" moments. After a while you start to get a feel for what things will look like once they are turned round.
I don't know if I've answered your question or not. Hopefully I've at least given you some food for thought. I find the journey is often more enjoyable than the destination.