Circles above a set size, in this case 1mm, will be ignored, and circles smaller will be drilled through. You can make circles out of lots or straight lines. Start off making your CAD DXF file using only straight lines and polylines, not arcs or rads. Look at my Links page for the free software I used. I like to edit and run it using Geany but it can be used with any text editor and started from a command line / terminal. It has no GUI ( Graphical User Interface ) but all paths and CNC machine settings can be edited as Python code is just a text file. It should (? I only have Linux ) run on any computer which has Python installed on it.
It turns any straight line into a machining / engraving moves and any circles less than a set size it drills a through hole.
I've been working on some Python code that converts DXF CAD ( Computer Aided Design ) files into G_Code that can be used on my CNC machine, mainly to produce PCBs ( Printed Circuit Boards ) but would also work for engraving text or for drilling the rows of holes in my LED Digital Clock Project.