Rapid prototyping (RP) is a widely used process in the industry to shorten development time.Another advantage of this technology is the ability to create conformal cooling systems, thus not only cooling time and cycle time can be shortened, but also shrinkage, thus warpage can be decreased. The main disadvantage of Rapid prototyping materials is their low thermal conductivity, which strongly influences cooling properties and warpage.The research based on a special developed injection mold for novel rapid prototyping based mold inserts with cooling systems. A method has been introduced to determine the most important thermal parameters for injection molding simulations using rapid tools. Those parameters, which can be measured such as the specific heat and thermal conductivity of the mold materials, are directly implemented into the software. The heat transfer coefficient between the polymer melt and the rapid tool insert surface cannot be measured in a reasonable way, thus simulation software was used to determine that based on indirect calculation 2 derived from real measurements. In the paper, the method was proved with Fused Deposition Modeling (FDM) and Polyjet mold inserts.