In order to make sure that the PCB will be possible to mills, use proper design rules for the Sherline.
The following is known to work:
Here is a design rule file for Eagle:
Any PCB design software can generate the Gerber and Excellon drill files.
In Eagle PCB, load this CAM file in the CAM processor to generate the files.
Start the Sherline mill up as described on sherline_cnc_mill.