| | Re: Help in Converting Stack to 3D image
I would recommend ImageJ. ImageJ is a free, open-source image manipulation package from the NIH and runs on any platform (Windows, Mac or Linux). Its functionality can be extended with plugins (see below).
Even more useful might be Fiji. As the name (Fiji Is Just ImageJ) suggests, it is simply ImageJ preloaded with large numbers of plugins, many of which are extremely useful for 3D reconstruction.
Either of these will let you register (align) the stacks, order them, crop them etc. They also do 3D-volume (but not, as far as I know, surface) reconstruction and can output a video of your 3D image slowly rotating and looking beautiful!
Hope that helps, there are many guides on how to use these packages out there - just google.