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Acid treatment of biomasses prior to energy generation can reduce the ash related problems by improving primarily heating value, ash and combustion characteristics. The aim of study is to determine the effects of acid treatment on the physiochemical structures of two different biomasses. Dilute (5 %wt) solutions of HCl, H₂SO₄ and CH₃COOH were used separately for treatment of rice husk and cotton stalk with time of 2 hours. H₂SO₄, being strong acid, exhibits comparatively significant changes in physiochemical structure of both biomasses as depicted by SEM micrographs and FTIR spectroscopy. In contrast, it assures the higher degree of ash removal and increase in heating values. Acid treated biomasses have shown more resistance toward thermal degradation.