Been planning this for a little while. I got a good deal on a plain edge Manix 2 a while back and wanted to have a go at making custom scales. Originally what I wanted was to use thicker scale material and get rid of the liners. I couldn't quite figure out what to do with the lanyard bushing though as I'm not set up to re-flare that and wasn't confident the linerless scales would grip the bushing very well. So I opted to keep the liners.
The Manix 2 scales are pretty simple since they're slabs with no recesses for liners. But they are also curvy and have a lot of holes and pockets that need to be in the right places. To overcome this I scanned the original scale on a scanner with some graph paper backing it (for scale). Then I took it into Fusion 360 and sketched around the scan.
That yielded a workable model pretty quickly:

I printed it out a few times to check everything was lining up. I probably would have had better luck with the fancy laser printers at work but I did this all at home on an inkjet. It got the job done but I'm not 100% sure how accurate the printer is in terms of absolute size.
The next step was to figure out how to cut this on the CNC mill. Fusion has pretty powerful CAM capabilities so this step was actually pretty quick. Basically you pick features and tell it to use a particular tool to mill or drill those features. The arrows show where the tools come in and out of the work piece.

I did a couple test pieces in some scrap wood and adjusted the model as needed. And then it was time to actually cut some scales. This takes about 45 minutes per scale. It could probably be closer to 15 minutes if I spent time dialing in the speeds. You can calculate very precise feeds/speeds for metals, but I've found very little reference for how fast to cut composite materials. I erred on the side of very slow. I used a 6mm end mill to face the stock to correct thickness and a 2mm endmill intended for PCB milling for the rest. Nothing too exciting here. I did take a video of one of the scales being machined but it's pretty boring.
Results!

This is some olive green linen micarta I got off ebay. It will look much darker when all polished up and sealed... I hope so at least.
Next up: a lot of sanding, test fitting, etc. And if anyone knows the correct way to finish micarta I'm all ears. I know to sand it pretty fine. I've heard some people wet it with mineral oil?