I clean them one by one under running warm water in the sink, no soap or detergent. I rub and squeeze them with my hands and until the white CA and other films are mostly gone. It works for me.
I cut up the larger pads to make three sets. I used the same set on ~50 pens, then forgot that set at a demo. My next set is still going strong. I still have one set unused set.
Hints:
* To save money, I buy the 3x4 inch pads and then cut them into smaller pieces to make multiple sets. You can get at least three sets of pads from them. I bought one set at the local Rockler; haven't needed more. The website shows them as gray, but they are colored same as the 2x2 pads. (3x4 Micro-mesh pads: $27.99, item #27940. The 2x2 pads are $19.99 #30710)
* Write dots on opposite edges of the pads with a Sharpie marker to make it easy to sort them in order. Put one dot on the edges of the first pad, two dots on the second pad, up to nine dots.
I tried drawing a "V" shape on each side of the stack, but found that the pads were much harder to sort, especially because the two Vs don't line up the same (the pad may be rotated left/right or flipped up/down, so getting the "V"s straight is hard. One V is easier, but then you have to arrange the pads with the marks on one side, and you still have a flipped up/down problem unless you draw a perfectly centered V, which is beyond me.
Use dots. Counting dots always works and you don't have to arrange the pads in any particular orientation.