How do I achieve a clean cut of small circles?
You have an easy one, I think. The best tool for cutting the holes you describe, in template plastic is a hole punch, also known as a circle punch. A quick search shows that Amazon has all three sizes you describe.
3/4&quot; - EK Tools circle cutter
1/4&quot; - &quot;Conventional&quot; hole punch - 0.25&quot;
1&quot; - Cady crafts Punch
All of the above are amazon links and you can certainly find other resources, but this should give you a path to take.