The invention comprises a method and apparatus for enhancing the analysis of noninvasive spectra, resulting in improved analytical performance. More particularly, the invention comprises a method and apparatus for processing noninvasive spectra with an analyte filter that preferably rejects variation likely to be detrimental to the measurement system, while passing signal that probabilistically is unique to the target analyte. Subsequently, the analyte filtered data are used to estimate an analyte property, such as a glucose concentration, in the presence of noise, interferences, state changes, and/or across analyzers.