Not 100% sure what you mean - if the multipass element is being saved to PNG, it should already have an alpha (assuming that is set in the save settings); you can also add an Alpha multipass element and save that, to use as a mask should you not be saving to PNG or have any other reason to want that separately. I am not sure if you mean multipass elements, or if you mean elements in the scene like specific objects - for the latter, you should be able to use an ID pass to identify the object and mask it out in post etc.
You can post an example of the multipasses you are saving, what the scene looks like, what you want to achieve, etc. Hope this helps though!