In the fabrication of plastic components with micro or nano structures, injection molding is one of the simple and most cost-effective processes. In the injection molding process, a complete filling of the micro or nano structures is necessary to fabricate a successful product. However, it is difficult to fully fill nano structures with an aspect ratio close to one or higher by the conventional molding process. In this study, mold inserts with nano channels were constructed by a LIGA-like process. The effects of the processing parameters and infrared heating on the filling of the nano structures were explored experimentally. Increasing the mold temperature, pressure, or filling rate did not improve the filling distance in nano channels with the conventional molding process significantly. Thus, an infrared mold surface heating system was introduced to assist the molding of the nano structures. To enhance the heating efficiency and reduce the cycle time, a heat-resistant layer was inserted under the mold cavity. The heat resistant plate led the heating system to work more efficiently. It easily increased the surface temperature over the glass transition temperature of plastic, thus fully filling the nano structures.