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I used Meshtool4 to add the envmap thing to my unit model, then added an alpha channel and made all but the visor of the model transparent, but the whole model is glossy ingame.
Any ideas?

Environment map does not work like specular map. It has no use for alpha layers at all, therefore you cannot mask out parts of the UV you don't want to be glossy. If you apply envmap to a specific MATD, then all MATI using that MATD will appear glossy.

Thanks AQT
New question.
How would I make a specific part of the model glossy?

It all depends on how the model was set up (in the program it was made in?). For example, the stock all_inf_tantive4trooper's helmet is set up as its own MODL; it has its own MATI, which references the MATD applied with environment map. So only the helmet is shiny. That's all I know. Hope this helps you somehow.