flashing the ECU is completely different from flashing the PC3.. The ECU sits under the seat (in its stock location). It has multipin connectors and is about 5 inches wide, 4 inches tall and about 1 inch thick. its black and probably has a rubber band that is holding it in place.
The pc3 is a fuel mapper, its job is to bypass the ECU's fuel mapping. The pc3 is red and black, is roughly 1 inch think 3 inches wide, 3 inches tall and is says on the box "Power Commander". It has 2 buttons to adjust fuel and a bar that shows current fuel richness.
The ECU and the PC3 can both be flashed... ECU flashing is more complicated than PC flashing and is not recommened if you do not already know what ECU flashing is
If the ECU has not been flashed you can remove the PC3 by taking off the cable that connects to the battery and also unplug the wiring harness adapters (make sure you plug the stock connectors back in or the bike will not run.
If you want to flash the Pc3 (if its firmware virsion is .18 or older) you can purchase a flashing tool from dynojet, just like the one i have sitting next to me.. or you can send your pc3 off to dynojet and they will do it for around 20 bucks. if its version .19 or newer you can download the software from dynojet and you can install it yourself using a mini USB cable (if its pc3 USB). if its pc3r contact dynojet...
What exactly are you trying to do?