There are several scenarios we can look at in terms of working with thicker materials.
The first important thing to consider is your tool length. It should be noted that no matter how high or low your Z-travel range is, you will only be able to cut as deep as your tool length will allow. The LongMill has approximately 4.9″ of Z-travel, but most tooling maxes out at around 2-2.5″ in length. In the large majority of cases, the limitation on how deep you can cut will come from the size of your tooling.
That being said, you can make certain adjustments to your LongMill to help cut materials of different thicknesses. The easiest option is to reposition your router in the mount by loosening the two front screws that hold the router and moving the router itself.
Secondarily, you can add spacers, such as a strip of MDF under the feet of the machine to raise the overall height of the machine.
In practice, the LongMill configured as per our instructions should be able to handle material up to 4″ thick. You may not need to make any modifications if you are not planning to cut materials that thick.