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We present the development and implementation of a novel wavelet shrinkage technique for the retrieval of obscured characteristic resonant signatures in the scattered terahertz (THz) reflectivity of molecular crystals. In this implementation, the wavelet basis functions associated with the absorption features were identified using the second-order total variation of the wavelet coefficients. Additionally, wavelet coefficients at certain scales were modified using the phase function corrections and wavelet hard thresholding. Reconstruction of the original spectra using these modified wavelet coefficients yielded the exact resonant frequencies of the chemicals, which were otherwise unrecognizable in the spectral artifacts of the rough surface scattering. We examined the robustness of this method over controlled levels of rough surface scattering, validated using the Kirchhoff approximation, in spectroscopic targets made from α-lactose monohydrate and 4-aminobenzoic acid (PABA), which have close spectral lines. We successfully retrieved the spectral absorption fingerprints in both specular and off-specular reflection geometries. This technique can be utilized for stand-off material characterization using the THz reflection spectroscopy in uncontrolled environments and potentially can be adopted for other broadband spectroscopic modalities.