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A new technique for analyzing the loss of high order modes in photonic crystal VCSEL is reported. The technique proposed is a semi-empirical approach that uses comparison to experimental data. For that purpose, photonic crystal VCSEL devices of single mode and multi mode are fabricated and measured for device characteristics comparison. The fabricated devices are modeled using finite difference frequency domain technique for the purpose of investigating the photonic crystal guided modes and loss analysis. In order to verify the findings, full three dimensional analyses are performed based on the fabricated single mode and multi mode devices structures using common finite difference time domain technique. The results show close agreement between the computed and experiment findings, justifying the used of the proposed semi-empirical technique for analyzing the loss of high order modes in photonic crystal VCSEL. Results for guided modes and near- and far-field are also presented for the photonic crystal VCSEL.