If I understood correctly, you need to make the arms (or another body part) invisible, right? If so:
1) Inside CC, you can go to the "edit mesh" function, and select the parts you don't want to appear, and then press "hide".
2) You can use photoshop (or any other editor) to create an opacity map of the body. You will load the diffuse map of the body in photoshop and you will fill the arms with black color, and the rest of the body with white. Then you will load this black-and-white image to your "opacity" channel. Remember, items that are painted black won't be visible, only white will be.
If something is not clear, tell me and I will elaborate. :)
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