If the machine makes a surface flat, it’s parallel to the machine. If one has a precision vise one takes the machined surface and puts it against the fix jaw of their vise. Machine. Two sides are now 90 degrees to each other. Rotate again and machine another surface. Rinse, repeat until done.
Here is a good video showing the method:
That is way things are done on a manual mill and this is just as true on a CNC machine.
A simpler version is to machine the top, flip 180 degrees. Now the flat surface is flat to the bed. Machine the top. Now the two sides are parallel. Rinse, repeat for the other pair of sides.
The nice thing about these methods is they work on any sized stock and any length end mill.
The key is to use as many precision surfaces as one has. With a precision vise, one has 2 or 3. IMHO the Nomad vise is not a precision vise… because I’m biased from using CMT vises which by themselves weight as much and cost as much as a Nomad.
A high end vise is square and flat to ~0.0001" or better and is trammed (squared) to the bed and mill. It takes a fair amount of time to get it “right” but once there…oh! it is so nice!
Machining a spoiler over the bed gives the Nomad one precision surface. The bed is pretty good but machining a spoiler flat takes the surface as far as the machine can go.
Attaching the vise to the bed one has a pretty darn good precision surface on the bottom of the vise; the fix jaw is pretty good.
These methods are designed to get the most one can get out of their machine. Many jobs do not require take your machine completely to edge of its abilities. Don’t go nuts unless one wants the absolute best they can get. Keep in mind machining wood to edge isn’t going to stay that way - changes in the wood happen with temperature and humidity.
The fun begins when we want to avoid doing 6 flips. If the machine is square and flat (trammed) one can mill the top and 4 sides to be 90 degrees to each other (assuming the end mill is perfectly straight). One flip and the bottom can be flattened along with the rest of the 4 sides.
This method is limited to the a bit less than twice the “stick out” of the end mill. Past that, we use the six flip method.
How to keep the X0Y0 through the flip is a discussion for another time. Hint: a jig.