Here's how I do it (in this example I'm shortening a titanium spoke, but the procedure for stainless steel spokes is the same):
- cut spoke using a good heavy duty set of pliers or side cutters;
- clamp spoke in spoke threading machine, but not all the way in - this way you can access the end of the spoke;
- file the spoke end flat and file a slight chamfer all round;
- move spoke fully into threading machine;
- thread spoke - I use a zip-tie on the shaft of the threading machine as a stop so I get about 10mm of thread on the spoke.