Preparation of high-quality boron nitride nanotubes (BNNTs) from commercially available stock is critical for eventual industry adoption and to perform comprehensive experimental studies of BNNTs. Separation of hexagonal boron nitride (h-BN) and BNNTs is a significant challenge, and equally so, quantification of h-BN content in mixed samples is a major challenge due to their nearly identical properties. This work introduces a simple method of quantifying h-BN content in BNNTs based on FTIR analysis. Quantification is achieved by “spiking” a BNNT sample with pure nanoscale h-BN as an internal standard. To demonstrate the efficacy of the quantification technique two BNNT enrichment methods, surfactant wrapping and centrifugation, and a novel sonication-assisted isovolumetric filtration are introduced. FTIR spectra of enriched samples show clear trends throughout the processes. We propose and demonstrate that FTIR peak ratios of the transverse and buckling modes of mixed h-BN/BNNT samples can be used to calibrate and quantify h-BN content in any BNNT sample. Hopefully, this method enables as-received BNNTs to be quantifiably enriched from low purity commercial feedstocks, enabling future development and study of BNNTs and related technology.