When using FreeSCAN, one of your options when writing programming to the scanner is to erase everything first. Choose that option, instead of the "add" or "replace" settings, and that will accomplish what you want.
If you really prefer to just erase everything first, then do this:
Turn the scanner off.
Then, press and hold down the 2, 9, and Hold keys while pressing the power button to turn back on. That will clear the scanner's programming memory. There is no effect on firmware or any applied upgrades.