We are studying the application of the electron cyclotron resonance ion source (ECRIS) for the new materials production on nano-scale. Our main target is the endohedral fullerenes. There are several promising approaches to produce the endohedral fullerenes using an ECRIS. One of them is the ion-ion collision reaction of fullerenes and aliens ions to be encapsulated in the mixture plasma of them. Another way is the shooting of ion beam into a pre-prepared fullerene layer. In this study, the new device configuration of the Bio-Nano ECRIS is reported which allows the application of both methods. The basic concept and the preliminary results using Ar gas and fullerene plasmas are described.