The authors present a new approach within advanced graphics simulations for the problem of nano-assembly automation and its application in medicine using collective robotics. The problem under study concentrates its main focus on autonomous control for nanorobot teams coordination as a suitable way to perform a large range of tasks and assembly manipulation in a complex environment. The presented paper summarizes distinct aspects of some techniques required to achieve a successful nano-planning system design for a large number of cooperating autonomous agents and illustrates their three dimensional visualization in real time.