You don't need to microwave it just needs to be heated but there are solutions that will allow for applying dies to any materials. Most synthetics will take dyes rather well, with some of my Maribou jigs, I've had great success obviously because of the nature of materials but for the tougher stuff like some wooly buggers that which usually contain Maribou, Chenille and the Saddle Hackle, as well as the wire.
Anyway there are a couple easy, safe ways to do it. Also don't plan to re dye the same fly all the time, you'll cause the materials deteriorate.
1) Rit is a great product.
2) KoolAid (which is why I've stopped drinking it, but then again as a kid who knew better?!)
3) Acid Dyes (Dharma Acid Dyes)
#1 Rit is pretty nice. Its about $4 a bottle which should last you forever, because its not like you are dying all the time.
#2 Is fairly obvious, if you got kids you'll probably have it around. But its only about $0.20 in the grocer? Trouble is you won't get much of a color selection.
#3 only requires hot water, its not gonna harm already tied flies. I have had access to this product via friends but you can order it and probably pick it up at walmart I am sure or any fabric place.
That or keep it simple and just buy more flies
You shouldn't have an issue with fading either, make sure you give it some reasonable time to dry. I usually throw mine above the furnace, for a day or two or till I am satisfied it's set well. you have to experiment a little with it, but its kinda a fun. I came across this when my favorite steelhead fly got hit with black splotches, something I had bled on to the fly and well...yeah >< kinda mad, but now its a show piece anyway, memento to my first steelie ever lol