No doubt you have your board making technique that you have perfected along the time and that you're religious about. I'm not lecturing you here nor saying that some methods are better. This is just a fast-forward DIY guide through the PCB manufacturing methods.
There are generally two directions. The first, the oldest but in no way the worst, involves removing regions from a copper-clad board leaving only the traces, footprints and other markings in place. Applying conductive material over an empty board is the second.
While the second is a lot quicker and eliminates some nasty processes, it yields a less robust product. However it suits well for prototyping purposes rather than long term uses.
Everyone wants to create boards that are resilient to mechanical and chemical factors, myself included. Therefore, I'll incline using the first method. In this case, again, there are two approaches. Mechanical isolation of the traces constitutes the first while the second makes use of chemicals for copper removal. It's up to each individual to weigh the advantages and disadvantages but unless you own or have access to a CNC routing machine, the chemical process is pretty much the only way to go.
The chemical process involves submerging your board in a corrosive agent that removes the exposed copper. This requires the use of a mask that should remain intact while exposed to the etching solution. Choosing the mask application method and the masking material constitutes the difficult part of this method. It can be drawn by hand using a permanent marker or adhesive plastic tape but can be automated with faster and better results.
Among the machine automated mask application techniques, the common DIY choices are the toner transfer and photo-litography, both yielding excellent results but requiring extra hardware and materials. The toner transfer requires certain control in temperature, pressure and the duration of the process. Any bias from the right values results in a poorly attached or smeared mask. Needless to say, some of the new and cheaper laser printers use a higher temperature toner making it a pain. The alternative requires a specially treated board and extra chemical and photographic processes. It seems that there are no easy alternatives.
What if instead of trying to apply a mask exactly where needed, we could apply a global protective coating from which we'd remove the regions to be exposed for etching. That would resemble to isolation routing except that instead of using a bit on a high speed spindle to remove copper, we're just using a pointed tip for carving the much softer coating. The tip scratching movement can be automated much easier and the process would be faster that the isolation routing.
This could be achieved by using a modified polar bot.