Written by Rabbis Eli Gersten, Yaakov Luban, and Moshe Zywica of the Orthodox Union
Best, of course, is to have two microwaves, one for milchigs (milk foods) and one for fleishigs (meat foods). But if that is not possible, one should designate the microwave for one use or the other. Then if, for example, one needs to warm something milchigs in their fleishig microwave, they should double wrap the food.
Unfortunately, this is not advisable for heating liquids in a microwave, because the buildup of steam will often cause the wrappings to burst. But dry items can be double wrapped, and even liquids can be double wrapped so long as they are only warmed.
One may use two plastic wraps or even a plastic wrap and a paper wrap. For example, one may place the plate of food into a ziptop bag and then place that bag inside a paper bag. It is preferable that the microwave be wiped clean first.
Similarly, in a non-kosher environment, i.e. an office, double wrapping a kosher product before using the microwave is the only way to guarantee the kosher integrity of the food.