If you machine without the G41 or G42 in your code, the program will take into account the center of the tool, regardless what is the diameter of your tool.
With the G41 or 42 code, the program will take the tool diameter into account.
So what you can do, put code in your program to get close where you start to machine.
Place the G41(climb milling) or G42(conventional milling) into your code.
Put the minus Z value you want
Machine your part.
Lift the Z
Put the G40(remove the offset diameter or the tool)
And that's it.
But mach3 must know what tool number you're using, and it's diameter
Just look at second picture, this is an example where to place the G41 or G42 code.
And take a look at this website, click on G41 or G42(white letter) This will explain better than me
http://www.cncezpro.com/gcodes.cfmHope this help, Jeff