Wiring harnesses often have unneeded wires, depending on the application. While it's perfectly acceptable to cut and insulate unused wires, the completist approach might involve actual removal of the unwanted pins holding the irrelevant wires in place. Tools exist for a variety of plug types, and since removal is relatively easy with the right pin pusher, it makes sense to perform the action. Excess wiring may be considered unsightly, or simply might add too much bulk to a tight installation.
Insert the pin extractor in the open end of the plug, over the pin requiring extraction.
Push the plunger down, depressing the barbs holding the pin in place.
Grab the wire as close to the back of the pin as possible. While still holding the barbs in, pull out the wire gently, taking the pin with it.
You can use a small No. 1 flathead screwdriver for flat pins, as opposed to purchasing a tool. Simply press down on the top of the tab while pulling the pin out with a pair of needle nose pliers.