When kashering my microwave, does it matter if the vessel is milchig or fleishig? What happens to the vessel when the microwave becomes kosher?
Several authorities have written that a microwave can be kashered by ensuring that it is completely clean, leaving it unused for 24 hours, and then turning on the microwave with a cup of water inside for several minutes (until an amount of water has evaporated). Note that the tray on which food is placed would require hagala, or replacement with another tray.
The cup used for a meaty microwave should be meaty, and for a milky microwave, milky. If the microwave is (possibly) tereif, a disposable cup should be used, which is discarded after the kashering procedure.
Sources: Shut Vehanchayot (of Rabbi Halperin, head of the Institute for Halachah and Technology; to be published in the near future), based on Shulchan Aruch, Yoreh Deah 92:8, 93:1 (Rema), 108:1 (and commentaries); Peri Chadash 121:15; Pri Megadim, Mishbetzos Zahav (beginning of) 94; Mitbach Kehalachah, pp. 55-88; Hamitbach Hakasher p. 82-3; Techumin, Vol. 8, p. 21.