Reheating furnace is an essential facility of a rod mill plant where a billet is heated to the required rolling temperature so that it can be milled to produce wire. Although it is very important to obtain information on billet temperatures, it is not feasible during furnace operation. Consequently, a billet temperature profile should be estimated. Moreover, this estimation should be done within an appropriate time interval for an on-line application. In this paper, a billet heat transfer model based on 2D FEM(Finite Element Method) with spatially distributed emission factors is proposed for an on-line billet temperature estimation and also a measurement is carried out for two extremely different furnace operation patterns. Finally, the difference between the model outputs and the measurements is minimized by using a new optimization algorithm named uDEAS(Univariate Dynamic Encoding Algorithm for Searches) with multi-step tuning strategy. The obtained emission factors are applied to a simulation for the data which are not used in the model tuning for validation.