hi i am useing a tga file with the alpha channel as pure black so for certain areas in my models to be transparent, however for some reason the whole model seems to be transparent (although you still see the color) not just the part were the texture is black, any ideas anyone?

I remember that some version of the mdl exporter needed to put the tga by MED editor after, because the exporter didn't do it!
But remember that flag "transparent" don't need to set.

If, nothing works, put a image here!

Just to make sure: If you want to see certain parts of the model, the alpha channel must be white there (or grey for semi transparency).
However, I had recently a similar case. It turned out, that I simply had forgotten to set up the UV mapping.

I have a similar discussion in the beginners section. Do a search there for "different type of transparency".