Due to the high etch rate and low fabrication cost, the wet etching of silicon using KOH etchant is widely used in MEMS fabrication area. However, anisotropic etch characteristic obstruct intuitional mask design and compensation structures are required for mask design level. Therefore, the accurate modeling for various types of silicon surface is essential for fabrication of three-dimensional MEMS structure. In this paper, we modeled KOH etch profile for MEMS based energy harvester using fuzzy logic. Modeling results are compared with experimental results and it is applied to design of compensation structure for MEMS based energy harvester. Through Fuzzy inference approaches, developed model showed good agreement with the experimental results with limited etch rate information.