I know there's Java3D, but from what I also know it's not fit for what I want to do, which is, based on a series of pictures to plot a 3D image on the screen. For instance lets say we have XX-XXXX (or more) pictures of a human face, we process them and then (using the points gathered in that process) we want to reconstruct it (the face) on the screen. Are there already libraries for that, or should I start working on my own? The whole thing would work with augmented reality and medical images.
The most commonly used method of drawing 3D in Java is JOGL. However it assumes you know the polygons and textures that you want to plot. There are also a number of game-oriented 3D engines such as LWJGL which provide more functionality, but basically you need to know the shapes you want to plot.
I know of no libraries that allow for reconstruction of a face based on 2D pictures.
If you want to create the algorithms yourself, and need a library to help create / render them, have a look at processing. Its a programming language / java library for 2D & 3D data visualization and image processing, simple but powerful, and well documented to boot.
I don't know exactly what form you want the generated face to be, but processing also supports mass (3D) particles.
See processing.org and openprocessing.org for whats possible.
If you want a full product / library that already does the whole process, akin to facegen (www.facegen.com) , I don't think there's a Java equivalent.