Here's how I use it.
I make the counters using Powerpoint. Draw squares or circles of the appropriate dimensions, and use the image to fill the object. If you're making multiples of the same monster, add numbers to the objects as well, nd fiddle with the textbox settings to get the number in a good place in the image, and with the font/size to make it look good. I find that Tahoma, Bold, 12 point works well.
For counters that will likely only be used once (e.g. "this session, they'll fight some goblins"), I just print them on regular paper. For ones that need more durability, I either print them on cardstock (300 gram paper), or on regular paper which I then glue to cardboard. I prefer the first option.
I have attached an example, the counters I made for the first part of Red Hand of Doom (spoilers for those who are going to play in the adventure). It is mostly made from CCDigital images, but a few are taken from the WOTC art galleries (and cropped to make good counters). I hope FDP don't mind me uploading it.