Can you be more specific? What do you mean under “transparent part of the alpha channel”? Alpha is transparency per definition. Please try to be more comprehensible otherwise you cannot get the answer you need.
Welcome on board! Try to illustrate the issue a bit clearer.
It also helps to know why you want to do it, there is often another way to achieve something.
Do you mean, so the object renders, it is seen in the RFW, but is black in the alpha channel, cutting out things behind it? This can be done with mental ray.
Use a Matte/Shadow/Reflection material. In the M/S/R’s Background slot, put the mr Camera Map shader. In the Camera Map shader, make sure Force Transparent Alpha is on, in the shader’s map slot (the small square one, not the long browse one) put a Material to Shader. In the material to shader, instance the material you want on the object. Apply the M/S/R material to the object.
If you are using scanline, it will be a two pass process. Render it as normal, then change the object’s material to Matte/Shadow, with Affect Alpha on, render again, then use the alpha channel from the second render and the RGB from the first.