You can use alpha/ 32bit textures (let's say from Photoshop or Gimp) and import them in MED (I suggest to leave "extern(al)" checked). However, then all of your model will be rendered in the transparent pass and sorting errors (with other objects, particles or on a polygonal basis) could appear.
If you only want to have let's say transparent windows on a car or a house you can use two or more skins and have the parts of the model with solid parts with corresponding 24bit textures first (assign the windows etc. to the last skin(s)). Your model then will be rendered in the solid and the transparent pass and should turn out fine.

Have a look here, too: http://opserver.de/swik10/index.php?title=Ent_mtlset