This is what it sounds like to me that you are trying to do: You have taken a picture of transparent objects and would like to remove the background and preserve the transparency of the foreground objects (so that perhaps you could replace the background with something else).
First thething is a choice you have to make: You can use built in tools to do the job as quickly as possible, but you sacrifice a lot of quality and realism. Or you can put in a little time and do it manually but with far better results. I would choose the latter ;)
If I had to pull that off I would probably shoot a white background to start with, then in Photoshop (or the equivalent):
- Cut out the negative space (the background that doesn't show through the bottles. Basically anything you can remove entirely from the image. Be careful to preserve hard edges so that the image looks realistic if you replace the background later.
- Make a new background layer that is black (you will delete it later to get your transparency back).
- Create a clipping mask for the bottles and whatever else is in the foreground. (After this all you should see is back because the clipping mask will be empty).
- Slowly brush in parts of the image by adding content to the clipping mask. Add opacity slowly. Make sure hard edges are completely opaque, areas where the color affects the background are semi-transparent, and areas where you could originally see the background are completely transparent.
That would be my workflow. I would also probably stick a semi-transparent copy of the original image between the background and the clipped image as a reference for the brush and then get rid of it later. If you want a perfect background replacement though, you are going to need to do a little touch up depending on what the background is to make reflections and diffractions look realistic. Best of luck!