A hyperspectral Fourier transform spectrometer (HS-FTS) has been developed to study biological material binding to surfaces through spatially resolved, spectral self-interference fluorescence microscopy and also label-free white light reflectance spectroscopy. Spectral self-interference fluorescence microscopy yields the height of fluorescent tags bound to a specific location on biomolecules tethered to a surface, and from this the biomolecule conformation can be predicted; white light reflectance spectroscopy yields the average height of an ensemble of biomolecules relative to the surface. The HS-FTS is composed of a small, step scanning Michelson interferometer made by Optra, Inc., a series of commercial off the shelf imaging lenses, and a 12-bit thermoelectrically- cooled CCD camera. The system operates over the 500 to 900 nm spectral range with user defined spectral resolution, thereby supporting use of a host of fluorescent tags or white light spectral windows. The system also supports near real-time hyperspectral cube acquisition via undersampling with the use of a spectral filter and user defined interferometer step increments. The overall approach offers flexible yet sensitive measurement capability for a variety of biological studies. Preliminary results are presented of both spectral self-interference fluorescence microscopy and white light reflectance spectroscopy measurements of artificial, photographically etched surfaces with feature heights on the order of 10 nm. Planned future work includes spectral self-interference fluorescence microscopy measurements of biomolecule conformation as manipulated by external electrical and magnetic fields as well as label-free white light reflectance spectroscopy measurements of DNA microarrays.