In the newest version of Mat16, v1.1, when you save a mat, a popup is created and there is a checkbox for transparency. (1.0 and possibly a few versions earlier had this option as well, but it was located in the options menu -- v1.1 has a revised interface thing)
I like that purple saber. To get that "glow" that everyone's talking about (not glowsabers), run a black line down both sides of the blade texture (in the up and down direction). Filtering will kick in and blend the solid purple into transparency. You may need to shrink the width of the texture to get a better-looking glow effect, but I haven't experimented there, so you're on your own as far as trial and error goes.
May the mass times acceleration be with you.