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An earlier step tells you to remove the zest in large strips using a vegetable peeler. So it would be very easy to remove from the ice cream base.
I'll bet you could use a microplane grater with this recipe if you don't have a regular vegetable peeler to take off the big strips of zest as directed in step one. The thing about this recipe is it is supposed to produce a very smooth end product; with the microplane zest, your resulting ice cream would have a little bit of texture, but if you don't mind that bit of zesty texture, I think it would be fine.
I used a wide vegetable peeler and then used tongs to remove the peel from the custard. I would recommend peeling in one strip to the extent that you can so that you don't have to fish around for the shorter strips of zest.