Alpha on .obj just like a .png

Hello, I hope someone can help me. I play a game called rust I just bougt substance painter to try and help me make better skins. I was just using the defuse.png file in Gimp and it wasn't that bad... Example if I take the defuse.png of a face mask paint on it copy a texture to it whatever if there is a part of it I don't want to show up be clear or see through I just use the wand and paint over it in alpha and when I load in the skin it looks like that part is missing how do I do that with an obj file in substance painter can someone please link a easy to folow video. thank you for your time.