One important approach to characterize full three-dimensional information is to simulate the etching process of a sample with subsurface damage reversely. The simulation starts from the morphology of the sample at a certain time when the subsurface damage can be opened totally. In the etching experiment, it is possible for us to get the surface morphology at any time. The paper presents a finite difference algorithm to simulate the morphology evolution in an etching process and by the finite difference algorithm the morphology of the sample at a specific time can be given. Comparison of the simulated morphology and measured one provides us the clue of improving the finite difference algorithm. In this paper, the accuracy can be calculated through comparing the simulation with experimental result, and the maximum error of subsurface damage will be calculated.