A conduction heat transfer process is enhanced by filling prescribed quantity and optimized-shaped high thermal conductivity materials to the substrate. Numerical simulations and analyses are performed on a volume to point conduction problem based on the principle of minimum entropy generation. In the optimization, the arrangement of high thermal conductivity materials is variable, the quantity of high thermal-conductivity material is constrained, and the objective is to obtain the maximum heat conduction rate as the entropy is the minimum. A novel algorithm of thermal conductivity discretization is proposed based on large quantity of calculations. Compared with other algorithms in literature, the average temperature in the substrate by the new algorithm is lower, while the highest temperature in the substrate is in a reasonable range. Thus the new algorithm is feasible. The optimization of volume to point heat conduction is carried out in a rectangular model with radiation boundary condition and constant surface temperature boundary condition. The results demonstrate that the algorithm of thermal conductivity discretization is applicable for volume to point heat conduction problems.