Do you mean to create a 3D image from a series of images from the confocal? If that's what you are looking for, maybe ImageJ could be useful. Check out this tutorial, page 38: http://digital.bsd.uchicago.edu/resources_files/ImageJ%20basics%20tutorial%20v2.pdf

Definitely, imageJ is great for this (you can work with stacks of images). Many tutorial do exist. And if you're lucky, there is a specialist in your university. It is an open-source software, and there are plenty of scientists willing to help all around the world, I'm sure!

I need to compile and mix various 3D images taken using confocal microscope.

The images has to be aligned and arranged in such a way that we should be able to track a particular point throughout.

Did you have a look at all the ImageJ tutorials? They should also have a forum, where people are nice, from what I've been told.