We designed and simulated a nano-biosensor to work in wet chemical optical processes for the determination and analysis of gaseous or liquid media. For this purpose, the optical properties of materials have been studied, and by creating the relationship between the refractive index of materials and other optical parameters, the measurement process was carried out. In this work, an optical filter based on the photonic crystal (OFPC) was used. By creating an active environment for the interaction between the substance and electromagnetic light, a situation to measure the properties of available substances in that active environment could be provided. Considering that the defect created in the OFPC may cause disruption in its operation, so the volume of the environment should be limited. Creation of defects in the structure of the nano-biosensors can increase the accuracy and quality of measurements; finally by rearranging the created defects, the output will be placed in the appropriate scope. The accuracy is increased by applying the finite difference time domain (FDTD) modeling approach in order to analyze the wave equations governing the structure of the photonics crystal.