The first thing a machinist asks when making a part is, “how do I hold it?” A lot of times a vise or collet chuck is a good answer. There are a lot of techniques. For holding a flat part, often a good answer is to bolt the part to the table or a surface plate.
Recently, in the machine shop, I needed to make some flat manifold plates for a customer. These were to be CNC milled out of 1/4 inch aluminum. The first step was to determine how they were to be held. As the parts do have bolt holes in them, I could have held the material down with clamps and then pre-drilled the bolt hole pattern. Then, I would have tapped holes in the fixture plate (which is just a scrap of aluminum I use for these sorts of projects) and bolted the material down. The only potential problem with that is that the bolts could mark the surface on the parts. I decided instead to put bolts into the material that would be cut away during machining.
By not using the bolt holes in the part, when I finished machining this job the part would not be held by anything. That is a great way to throw it through a safety shield and bust an endmill. Not good. I used a technique where the part would be held with thin tabs at intervals around the part. My CAM system has the ability to put those in automatically, but if you are manually programming or editing g-code, all you would need to do is pick a spot on the final depth and have the cutter jump up. In this case, I used .025 as a tab thickness, and half inch wide.
This is what the part looked like while still bolted into the CNC. 
Notice that the part stays together with the remainder material even after I unbolt it.
You have to be careful when choosing your tabs; if they are too thin, they will break during machining and the part will move, possibly wrecking it or damaging something else. If they are too thick, it will be difficult to remove the part from the stock. It should be noted also that the endmill moving up the side of the part like that WILL leave a witness mark. In this case, it really didn’t matter. This could have been minimized by having the CNC make more passes around the part, and then a finish pass that only skimmed over the tabs. The machinist has to decide what’s important for those considerations; I chose speed.
Anyway, that’s just another tip from the machine shop. If anyone has any questions, feel free to contact me.
CNC Machining 