Torque 2D question

Im in the process of making a 2D rpg and Im trying to figure out a good workflow for making the characters. I know about the torque tool that converts 3D animated models into the sprites but I dont need it. I have have blender to use. But I wanted to know how exactly I go about making transparency around the characters so the outlines around their bodies are encompassed by the environments and not the square of the whole tile. I'm using Blender and Gimp. Any help or suggestions are greatly appreciated. Thanks.