There are two options for this increment, option one is to develop the 3D viewer from scratch and option 2 is to integrate an existing molecule viewer.
The 3D model is contained within a file within the work directory called "current.xyz" it is a text file containing the number of each atom, the type of atom, x, y and z coordinates of each atom and a list of atom numbers that each atom is linked to.
To create a 3D viewer from scratch would be a mammoth task taking up more time than would be required to complete the whole project, it can be achieved using the Java3D framework that allows for the generation of 3D graphics using OpenGL.
The other option is to avoid re-inventing the wheel and integrate and existing 3D molecule view such as MolyView, CanvasMol or Jmol the problem with this approach is finding one that has an API compatible with Java, which will work on multiple platforms, and has a license compatible with GPLv3.