The general way of taking "truma" {the part of the crop that goes to the priest} is by physically removing that percentage of the crop. The same goes for "maaser" the tenth that is given to the Levi (a person descended from the tribe of Levi from his father's side.) This is what I think made the Rambam explain the mishna in Tracatate Trumah in a kind of forced way that does not seem to be in accord with its simple explanation.
The Mishna in Truma (ch 4) says simply
המפריש מקצת תו''ם מוציא ממנו תרומה עליו אבל לא למקום איר אחר ר''מ אומר אף מוציא ממנו תרומה על מקום אחר

 "When one separates a part of truma and maaser from a stack of grain, one can not take from it ("it" masculine gender) truma and maaser to another place but only to itself.  R. Meir says: Also to another place.
The simple explanation is like the Raavad  that since the part he separated is not the full amount [percentage] thus the entire stack is still mixed with "tevel" {unfixed grain that has not had truma and maaser separated from it yet.}  The reason is the general rule held by the sages אין ברירה ["No choice" i.e. "There is no reverse choice".] That means he can not take from the stack of grain one Seah {one measure} and then say this seah is maaser for 9 seah in this other stack. The reason? We can not say that in reverse there is choice to say what he now holds is tevel.            
This is certainly what the mishna sounds like and it goes well with the fact that R Meir says he can do so because R Meir hold יש ברירה, "There is reverse choice."
But then the obvious question is then the same problem exists for that very same stack of grain. Why can he take a seah and say "This seah is maaser for 9 seah in the stack?" If אין ברירה then אין ברירה. If there is no choice then there is no choice.

So the Rambam in Laws of Trumah ch 3:7 says when one separates a partial amount of truma he has to take truma from it (from the grain he separated.) That is to say it does not have the category of truma at all.

The question then the achronim [later authorities] ask is then what about the preious law in the Rambam ch 3:6 where it says if he separates 1/61 what he has separated is truma and he then goes and take the remaining amount that is needed to complete the right percentage of 1/60? [1/60 is a drop more than 1/61].
The Rash (Rabainu Shimshon (grandson of Rashi)) brings the Yerushalmi  that asks on the contradiction between the two mishnas these halachot are built on and it says in the later case he intends to separate more. This the Rash says means when he does not intend to separate more, the part he has separated is straight "tevel" and does not have the category of truma at all.
[I have not worked this all out but my question here is this: Is it possible the Rambam holds with this Rash?] 
I mean halaca 7 would be when he does not intend to separate any more and halaca 6 is when he intended to separate a complete percentage but missed by a drop?
I saw that Rav Shach explains the Rambam exactly the opposite from the Rash and I am wondering why this is necessary? That is Rav Shach says the Rambam holds when he does not intend to separate any more it has the full category of truma and maaser and when he does intend to separate more it does not because truma and maaser do no work in reverse. Then halaca 6 is simply not a case of working in reverse but of simply then and there not separating enough at one time.