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Maybe I am misunderstanding the question but if you are looking through a mil dot scope that is set at the mil setting its 36" from center of dot to center of dot. If your target is 3 feet then it would cover one mil at 100 yrds when looking through the scope.
To figure out what setting your scope needs to be at for the "mil setting" you could get a 36" target and put it at 100 yrds then look through your scope and zoom it until it covers exactly 1 mil.
With the scope set to it's milling setting, (mine is a 6x24 tasco, and the mil setting on it is 8 power)one mil at 100 yards is 3.6 inches if I remember right. Total of 10 mils in the reticle itself, so from the edge of the bar to the edge of the other bar would be 10 mils or 36 inches.
It is very simple once you get the mil dot master and read the manual. Once you know approximate size of your target, you estimate mil's and feed that information into the mil dot master and it will give you a range to target, knowing your range(you should know the drop at most given ranges) then it will tell you how many mils to hold over your target. Very simple stuff here, you can also compensate for windage with this system. Once you start using it, it is an awesome deal, I really enjoy mine, and the only reason I use my rangefinder anymore is to verify confirmed shot distances...the mil dot is the way to go in my opinion.