There is probably nothing new here, but I wanted to share the way I print not so simple PCB's always perfect without a single failure.
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Step 1: Circuit Design.
I always model the circuit in a breadboard to make sure everything works as expected. I will use the same components for the final circuit.
Step 2: Modelling.
In order to design the PCB, I first model the circuit in Proteus, and once everything is properly connected, launch ARES for track design, making sure the tracks are as wide as possible. Manual tweaking of the tracks is useful for this purpose and sometimes rerouting is also needed. Don't stick with the automatic design.
Step 3: Printing the Circuit Layout.
It is critical to laser print the circuit on a thin glossy magazine paper (the normal paper for most newsstand magazines). Normally this kind of paper is too thin for the laser printer to handle, so I tape it to a regular sheet of paper, that way it works fine. Be careful NOT to print the track design mirrored and just print the copper side artwork.
Step 4: PCB Preparation.
Cut the board to the desired size, as well as the printed layout. Try not to touch the printed surface with the fingers, handle the paper by the edges. Clean the copper side of the board throughly using ultra fine sand paper or metal wool and rub with pure acetone. Now you can put together the printed paper and the board.
Step 5: Layout Transfer.
Place a cold regular clothing iron in top of the paper side. The iron temperature SHOULD be set at around 120 Celsius not too much colder or hotter (in my iron it is the SILK setting, or between the NYLON and POLYESTER settings). The idea is only to make the toner in the print soft and sticky, but not to melt it down. With the iron in place turn it on and, without moving, just apply pressure till it reaches the temperature setting. I then start moving the iron in circles applying gentle pressure for three to five minutes. At the end you will notice the circuit design through the paper. Turn off the iron and let the PCB cool down for a while.
Step 6: Finishing the Transfer.
Once cool, place the PCB in a tray with water. After just a few minutes you will notice that the paper turns loose and the toner has transfered completely to the copper. There is no need to rub the paper to remove it. The PCB is then ready for the chemical treatment.
Step 7: PCB Finishing.
The PCB con be treated chemically for copper removal by your preferred method. I use ferric chloride but a mixture of muriatic acid and oxy-water also works. Once the etching process finishes (between 20 and 30 minutes), remove the toner with acetone. I use a 0.8 mm drill bit for all the holes and then a 1 mm bit for the larger electronic components. This way the finished circuit works perfect without the need to rework the tracks in any way.