If one removes the jumper while codes are being pulled, it should clear the codes.
I find it easier often to clear the KAM while at it (to evaluate what codes return after the puter starts fresh) so disco'ing the battery works better IMHO. Personal preference.
Sorry RC, allow me to clarify. When you use the code scanner. If you just plug it in and turn the key to the run position as MysteryMachine suggested and get out of your car to read the code reader, that's only good for the KOEO (Key On Engine Off) codes. If you want to run the running test on sensors, you need the KOER (Key On Engine Running) codes that may require you to operate the accelerator cable at a specific time. I was suggesting that both would be easy if you had (or made) and extension cable to do this.