The Boron Nitride Nanotube (BNNT) is capable of sensing the masses even below the zeptogram level when it is used as a resonator. The surface of BNNT is considered to be straight in most of the existing literatures. In this work, wavy surface of BNNT is considered, and its effect on the mass sensing capabilities of BNNT is investigated. A nonlinear mathematical model is developed by applying the continuum mechanics approach on surface deviated (wavy) BNNT of a hollow cylindrical geometry with thin wall. The model is normalized to the nanoscale level, and the degrees of nonlinearity arise due to waviness are identified in BNNT mass sensing application. The deformation in nanostructures is nonlinear that causes oscillations of large amplitude. The midplane stretching and waviness factor of a single walled BNNT, which is clamped at both of its end, are considered to investigate its frequency response to the attached mass. It is proposed to include waviness surface of BNNT to develop more accurate biomass sensor. It is further found that there is a shift in the resonance frequency due to surface waviness of BNNT as compared to straight BNNT. The future perspective of this study is to investigate methods to optimize the wavy structure of BNNTs for improved biomolecule detection. This could involve studying the effect of different wave patterns, sizes, and amplitudes on the sensor's sensitivity and selectivity.